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Opened 41 hours ago
#20547 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Savin the session
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> lighting simple
> lighting soft
> lighting simple
> set bgColor white
> set bgColor black
> help help:quickstart
> show cartoons
> style stick
Changed 0 atom styles
> style stick
Changed 0 atom styles
> style sphere
Changed 0 atom styles
> style ball
Changed 0 atom styles
> color bychain
> color bypolymer
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> ui mousemode right select
> ui mousemode right rotate
> open 8w6eb fromDatabase eds format ccp4
Fetching url http://www.ebi.ac.uk/pdbe/coordinates/files/8w6eb.ccp4 failed:
<urlopen error [Errno 11001] getaddrinfo failed>
> open 8w6e fromDatabase pdb format mmcif
Cannot open '8w6e': [WinError 10054] An existing connection was forcibly
closed by the remote host
> open 8w6e fromDatabase pdb format mmcif
Summary of feedback from opening 8w6e fetched from pdb
---
notes | Fetching compressed mmCIF 8w6e from http://files.rcsb.org/download/8w6e.cif
Fetching CCD KY6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/KY6/KY6.cif
8w6e title:
De novo design of HBC599 binder [more info...]
Chain information for 8w6e #1
---
Chain | Description
A B | HBC599 in complex with wFAP1.1
Non-standard residues in 8w6e #1
---
KY6 —
4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile
8w6e mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> open 8w6eb fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "8w6eb"
> hide bonds
> undo
> hide /A
[Repeated 1 time(s)]
> undo
> hide /a
> hide /b
> hide /c
> hide /
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /d
> select ~sel & ##selected
Nothing selected
> show /a
> hide /a cartoons
> select ~sel & ##selected
Nothing selected
> show /b
> show /c
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> hide /a cartoons
> hide /b cartoons
> hide /b
> show /c
> show /d
> show /e
> foldseek
Missing or invalid "chain" argument: empty atom specifier
> color bychain
> ui mousemode right select
> select /A:201@H071
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right "rotate slab"
> ui mousemode right "move planes"
> ui mousemode right "rotate slab"
> ui mousemode right "move planes"
> ui mousemode right "color key"
[Repeated 1 time(s)]
> key delete
> ui mousemode right "translate selected models"
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide /a cartton
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /a cartoons
> select ~sel & ##selected
Nothing selected
> hide /a
> hide target m
> undo
> save C:\Users\Public\Desktop\image1.png supersample 3
Permission denied writing file C:\Users\Public\Desktop\image1.png
> save C:\Users\Public\Desktop\image1.png supersample 3
Permission denied writing file C:\Users\Public\Desktop\image1.png
> cd "C:/Users/moham/Downloads/Chimera Testing Grounds"
Current working directory is: C:\Users\moham\Downloads\Chimera Testing Grounds
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image1.png"
> supersample 3
> ui tool show "Build Structure"
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image2.png"
> supersample 3
> ui tool show "Model Loops"
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image3.png"
> supersample 3
No alignments chosen for modeling
> /a
Unknown command: sequence /a
>
Incomplete command: sequence
> help
Unknown command: sequence help
> ui windowfill toggle
[Repeated 1 time(s)]
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> view #1.1 clip false
> sequence chain /A
Alignment identifier is 1/A
> select clear
> ui mousemode right select
> select clear
> select /B:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> sequence chain /B
Alignment identifier is 1/B
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:35
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /B:0
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:0-163
1387 atoms, 1393 bonds, 1 pseudobond, 161 residues, 2 models selected
> ui tool show "Model Loops"
> modeller refine 1/B:1:all-missing numModels 1 fast false adjacentFlexible 1
> protocol standard
Webservices job id: MU2YCO30IQ3GDOBB
Webservices job finished: MU2YCO30IQ3GDOBB
Modeller job (ID MU2YCO30IQ3GDOBB) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8w6e, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 863.2
RMSD between 161 pruned atom pairs is 0.138 angstroms; (across all 161 pairs:
0.138)
Associated chain_B chain B to chain B with 0 mismatches
Chain information for chain_B #3.1
---
Chain | Description
B | No description available
> select clear
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> select clear
> undo
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> ui tool show "Model Loops"
> select add #3
1506 atoms, 1520 bonds, 170 residues, 2 models selected
> remove'
Unknown command: remove'
> remove
Unknown command: remove
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete model chain_B_models
Missing or invalid "atoms" argument: invalid atoms specifier
> close #3
> ui tool show "Model Loops"
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
No alignments chosen for modeling
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /B:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Model Loops"
No alignments chosen for modeling
> /sel B:37-39
Unknown command: /sel B:37-39
> /select B:37-39
Unknown command: /select B:37-39
> select /B:37-39
Nothing selected
> select /B:37-40
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /B:37-39
Nothing selected
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "Unknown error
0xe0000225."
[Repeated 7 time(s)]
> ui tool show "Model Loops"
> select /B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /B:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Model Loops"
No alignments chosen for modeling
> select /B:40
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> sequence chain /A
Alignment identifier is 1/A
> select /A:0-1
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:0-1
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:1-36,41-79,82-118,125-161
1287 atoms, 1288 bonds, 149 residues, 1 model selected
> select clear
> select /A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:162-163
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:119-121
25 atoms, 24 bonds, 3 residues, 1 model selected
> select /A:0
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:0-163
1368 atoms, 1372 bonds, 2 pseudobonds, 159 residues, 2 models selected
> select /A:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:42-77
294 atoms, 293 bonds, 36 residues, 1 model selected
> select /A:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:36-41
25 atoms, 23 bonds, 1 pseudobond, 3 residues, 2 models selected
> ui tool show "Model Loops"
> modeller refine 1/A:1:internal-missing numModels 1 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: 7Q0V0YP1MSTL0AX5
Webservices job finished: 7Q0V0YP1MSTL0AX5
Modeller job (ID 7Q0V0YP1MSTL0AX5) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8w6e, chain A (#1) with chain_A, chain A (#), sequence alignment
score = 830.8
RMSD between 159 pruned atom pairs is 0.045 angstroms; (across all 159 pairs:
0.045)
Associated chain_A chain A to chain A with 0 mismatches
Chain information for chain_A #2.1
---
Chain | Description
A | No description available
> select #1/B:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select #2.1/A:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> close #2
> sequence chain /B
Alignment identifier is 1/B
> ui tool show "Model Loops"
> select /B:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:5-47
343 atoms, 343 bonds, 1 pseudobond, 40 residues, 2 models selected
> modeller refine 1/B:1:internal-missing numModels 1 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: EC2447KD0UUXRKVS
> select /B:5-47
343 atoms, 343 bonds, 1 pseudobond, 40 residues, 2 models selected
Webservices job finished: EC2447KD0UUXRKVS
Modeller job (ID EC2447KD0UUXRKVS) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8w6e, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 833.2
RMSD between 161 pruned atom pairs is 0.045 angstroms; (across all 161 pairs:
0.045)
Associated chain_B chain B to chain B with 0 mismatches
Chain information for chain_B #2.1
---
Chain | Description
B | No description available
> select clear
> view #2 clip false
> rename #2 8w6e
> close #1
> rename #2 id #1
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> fetch 8w6e
Unknown command: fetch 8w6e
> getcrd 8w63
Missing or invalid "atoms" argument: invalid atom specifier
> getcrd 8w6e
Missing or invalid "atoms" argument: invalid atom specifier
> open 8w6e fromDatabase pdb format mmcif
8w6e title:
De novo design of HBC599 binder [more info...]
Chain information for 8w6e #2
---
Chain | Description
A B | HBC599 in complex with wFAP1.1
Non-standard residues in 8w6e #2
---
KY6 —
4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile
8w6e mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select clear
[Repeated 1 time(s)]Drag select of 95 atoms, 89 residues, 2 pseudobonds, 79
bonds
> select clear
[Repeated 1 time(s)]
> ui mousemode right rotate
> clear
Unknown command: clear
> delete all
> open 8w6eb fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "8w6eb"
> open 8w6e fromDatabase pdb format mmcif
8w6e title:
De novo design of HBC599 binder [more info...]
Chain information for 8w6e #2
---
Chain | Description
A B | HBC599 in complex with wFAP1.1
Non-standard residues in 8w6e #2
---
KY6 —
4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile
8w6e mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> ui mousemode right select
Drag select of 125 atoms, 161 residues, 1 pseudobonds, 108 bonds
> select /B:82
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select /B:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right select
> select
> ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
2755 atoms, 2765 bonds, 3 pseudobonds, 320 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> delete /a
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel cartoons
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> select clear
> delete al
Missing or invalid "atoms" argument: invalid atoms specifier
> delete all
> open 8w6e fromDatabase pdb format mmcif
8w6e title:
De novo design of HBC599 binder [more info...]
Chain information for 8w6e #2
---
Chain | Description
A B | HBC599 in complex with wFAP1.1
Non-standard residues in 8w6e #2
---
KY6 —
4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile
8w6e mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> delete /b
> select clear
> /b
Unknown command: sequence /b
> /a
Unknown command: sequence /a
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image4.png"
> supersample 3
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image1.png"
> supersample 3
> select clear
> close #1
> ui tool show "Model Loops"
> sequence chain /a
Alignment identifier is 2/A
> ui tool show "Model Loops"
> modeller refine 2/A:1:internal-missing numModels 1 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: 8O4OUE99BAV2BD6N
> select clear
Webservices job finished: 8O4OUE99BAV2BD6N
Modeller job (ID 8O4OUE99BAV2BD6N) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8w6e, chain A (#2) with chain_A, chain A (#), sequence alignment
score = 830.8
RMSD between 159 pruned atom pairs is 0.045 angstroms; (across all 159 pairs:
0.045)
Associated chain_A chain A to chain A with 0 mismatches
Chain information for chain_A #1.1
---
Chain | Description
A | No description available
> select clear
> ui tool show "Model Loops"
> close #2
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image1.png"
> supersample 3
> open 8w6e fromDatabase pdb format mmcif
8w6e title:
De novo design of HBC599 binder [more info...]
Chain information for 8w6e #2
---
Chain | Description
A B | HBC599 in complex with wFAP1.1
Non-standard residues in 8w6e #2
---
KY6 —
4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile
8w6e mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> delete /b
> close #1
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image2.png"
> supersample 3
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> color red
> select clear
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> color sel red
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> color sel red byatom
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel byatom
> select
> ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
1368 atoms, 1372 bonds, 2 pseudobonds, 159 residues, 2 models selected
> color sel red
> color sel white
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select clear
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> color sel byelement
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
1368 atoms, 1372 bonds, 2 pseudobonds, 159 residues, 2 models selected
> color (#!2 & sel) magenta
> color (#!2 & sel) medium blue
> color (#!2 & sel) cyan
> color (#!2 & sel) yellow
> select clear
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image3.png"
> supersample 3
> surface
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image3.png"
> supersample 3
> hide target a
> surface hidePatches
> hide #2.2 models
> show #2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2 models
> show #!2 models
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel bynucleotide
> color sel byhetero
> color sel bychain
> color sel bypolymer
> rainbow sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue KY6 (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.12/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\moham\AppData\Local\Temp\tmp0cikg8gm\ante.in.mol2 -fi mol2 -o
C:\Users\moham\AppData\Local\Temp\tmp0cikg8gm\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n
(KY6) ``
(KY6) `Welcome to antechamber 20.0: molecular input file processor.`
(KY6) ``
(KY6) `Info: Finished reading file
(C:\Users\moham\AppData\Local\Temp\tmp0cikg8gm\ante.in.mol2); atoms read (43),
bonds read (45).`
(KY6) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(KY6) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(KY6) `bash.exe: warning: could not find /tmp, please create!`
(KY6) ``
(KY6) ``
(KY6) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(KY6) `bash.exe: warning: could not find /tmp, please create!`
(KY6) `Info: Total number of electrons: 188; net charge: 0`
(KY6) ``
(KY6) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`
(KY6) `bash.exe: warning: could not find /tmp, please create!`
(KY6) ``
(KY6) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX 1.12/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(KY6) `bash.exe: warning: could not find /tmp, please create!`
(KY6) ``
(KY6) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/atomtype" -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(KY6) `bash.exe: warning: could not find /tmp, please create!`
(KY6) ``
Charges for residue KY6 determined
Coulombic values for 8w6e_A SES surface #2.3: minimum, -1.96, mean 0.29,
maximum 3.25
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> color sel bynucleotide
> color sel byhetero
> rainbow sel
> coulombic sel
Coulombic values for 8w6e_A SES surface #2.3: minimum, -1.96, mean 0.29,
maximum 3.25
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 8w6e_A SES surface #2.3: minimum, -1.96, mean 0.29,
maximum 3.25
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel bychain
[Repeated 1 time(s)]
> hide sel surfaces
> color sel bynucleotide
> color sel byhetero
> select ~sel & ##selected
1390 atoms, 1372 bonds, 2 pseudobonds, 181 residues, 2 models selected
> select ~sel & ##selected
43 atoms, 45 bonds, 1 residue, 1 model selected
> color sel byatom
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> select /A:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASP"::name="GLU"::name="GLY"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
1368 atoms, 1372 bonds, 2 pseudobonds, 159 residues, 2 models selected
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right select
Drag select of 43 atoms, 159 residues, 2 pseudobonds, 45 bonds
> split
Did not split 8w6e, has only one piece
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> split
Did not split 8w6e, has only one piece
> split
Did not split 8w6e, has only one piece
> select clear
> split #2
Did not split 8w6e, has only one piece
> select ::name="KY6"
43 atoms, 45 bonds, 1 residue, 1 model selected
> split #2 atoms sel
Split 8w6e (#2) into 2 models
Chain information for 8w6e 2 #2.2
---
Chain | Description
A | No description available
> hide #2.1 models
> show #2.1 models
> hide #!2.2 models
> show #!2.2 models
> select clear
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.2.1 models
> show #2.2.1 models
> hide #!2.2 models
> show #!2.2 models
> rename #2.1 ligand
> rename #2.2 protein
> select clear
> show surfaces
[Repeated 1 time(s)]Drag select of protein_A SES surface, 557 of 180008
triangles, 6 residues
> select clear
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right zone
> ui mousemode right rotate
> ui mousemode right "clip rotate"
Drag select of protein_A SES surface, 25 of 180008 triangles, cap front, 29 of
8834 triangles
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image4.png"
> supersample 3
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image5.png"
> supersample 3
[Repeated 1 time(s)]
> select add #2.1
43 atoms, 45 bonds, 1 residue, 2 models selected
> hide sel surfaces
> select add #2.2
1433 atoms, 1417 bonds, 2 pseudobonds, 182 residues, 4 models selected
> select subtract #2.1
1390 atoms, 1372 bonds, 2 pseudobonds, 181 residues, 3 models selected
> select subtract #2.2
1 model selected
> select add #2.2
1390 atoms, 1372 bonds, 2 pseudobonds, 181 residues, 2 models selected
> hide sel surfaces
> ui tool show H-Bonds
> hbonds #2.1 target #2.2 reveal true color red
Expected a keyword
> ui tool show H-Bonds
> hbonds reveal true
196 hydrogen bonds found
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> slice
Unknown command: slice
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "Unknown error
0xe0000225."
[Repeated 5 time(s)]
> clip 2.2 on
Expected a keyword
> clip #2.2 on
Expected a keyword
> show sel surfaces
> ui mousemode right clip
> ui mousemode right select
Drag select of protein_A SES surface, 31022 of 180008 triangles, 26 atoms, 27
bonds, 39 residues, 29 pseudobonds
> select clear
> clip #2.2 on
Expected a keyword
> clip #2.2
Expected a keyword
> clip #2.2 thickness 10
Expected a keyword
> clip #2.2 thickness 10
Expected a keyword
> clip #2.2 on
Expected a keyword
> clip model #2.2 true
Drag select of protein_A SES surface, 3731 of 180008 triangles
> select clear
> ui mousemode right clip
> clip model #2.2 true
> ui mousemode right clip model #2.2 on
> mousemode rightMode clip model #2.2 on
Expected a keyword
> clip model #2.2
Model #2.2 clipping True
Model #2.2.1 clipping True
Model #2.2.2 clipping True
Model #2.2.2.1 clipping True
Model #2.2.3 clipping True
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> clip model #2
Model #2 clipping True
Model #2.1 clipping True
Model #2.1.1 clipping True
Model #2.2 clipping True
Model #2.2.1 clipping True
Model #2.2.2 clipping True
Model #2.2.2.1 clipping True
Model #2.2.3 clipping True
> clip model #2.1 false
> ui mousemode right clip
> ui mousemode right select
> ui mousemode right clip
> ui mousemode right select
> ui mousemode right clip
> clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select clear
> select add #2.1
43 atoms, 45 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
[Repeated 1 time(s)]
> view sel
> ui mousemode right "clip rotate"
> ui mousemode right translate
> color #2.2 #140cffff
> color #2.2 #ff2aadff
> select clear
> volume projectionMode rays
No volumes specified
> volume projectionMode rays
No volumes specified
> volume projectionMode rays
No volumes specified
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> save "C:\Users\moham\Downloads\Chimera Testing Grounds\image6.png"
> supersample 3
> lighting simple
> save "C:/Users/moham/Downloads/Chimera Testing Grounds/wFAP.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1475, in take_snapshot
'ses_id': self.structure.session_chain_to_id(self._c_pointer),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'session_chain_to_id'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A':
Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'chain A': Error
while saving session data for 'tools' -> [, , , , ] -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1475, in take_snapshot
'ses_id': self.structure.session_chain_to_id(self._c_pointer),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'session_chain_to_id'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A':
Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'chain A': Error
while saving session data for 'tools' -> [, , , , ] -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save "C:/Users/moham/Downloads/Chimera Testing Grounds/wFAP.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1475, in take_snapshot
'ses_id': self.structure.session_chain_to_id(self._c_pointer),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'session_chain_to_id'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A':
Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'chain A': Error
while saving session data for 'tools' -> [, , , , ] -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1475, in take_snapshot
'ses_id': self.structure.session_chain_to_id(self._c_pointer),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'session_chain_to_id'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A':
Error while saving session data for 'tools' ->
[<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0>,
<chimerax.model_panel.tool.ModelPanel object at 0x000001EC29F276D0>,
<chimerax.cmd_line.tool.CommandLine object at 0x000001EC2434CB90>,
<chimerax.log.tool.Log object at 0x000001EC243393D0>,
<chimerax.toolbar.tool.ToolbarTool object at 0x000001EC29F8E9D0>] ->
<chimerax.seq_view.tool.SequenceViewer object at 0x000001EC4BCD2BD0> ->
<chimerax.atomic.molobject.Chain object at 0x000001EC4CB08510> 'chain A'
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'chain A': Error
while saving session data for 'tools' -> [, , , , ] -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2135
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.11.9
Locale: en_US.cp65001
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Latitude 5400
OS: Microsoft Windows 11 Pro (Build 26200.8655)
Memory: 16,985,047,040
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz
OSLanguage: en-US
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2026.5.20
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2026.2
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
WMI: 1.5.1
yarl: 1.24.2
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