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#19460 closed defect (can't reproduce)
H-Bonds: More than 2 coplanar positions specified
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.5.8-1.el8.elrepo.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.3rc202111090815 (2021-11-09 08:15:14 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3rc202111090815 (2021-11-09)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/shabir/Topos_CTD/ATPase_CTD/RealSpaceRefine_8/SpTopoIV_ATPase_CTD_X-
> cryoEM_RSR24_rsr_007-coot-0_real_space_refined_008.pdb format pdb
Chain information for SpTopoIV_ATPase_CTD_X-
cryoEM_RSR24_rsr_007-coot-0_real_space_refined_008.pdb #1
---
Chain | Description
A | No description available
C | No description available
D | No description available
> close
> open /home/shabir/Topo_EM_figs/T14mer_B-DNA.pdb
> /home/shabir/Topo_EM_figs/E26mer_B-DNA.pdb
> /home/shabir/Topo_EM_figs/side_J484_rsr7.pdb
> /home/shabir/Topo_EM_figs/front_J479_rsr9.pdb
> /home/shabir/Topo_EM_figs/SpTopoIV_8qmb5j5pq_on_4i3h-rev.pdb
> /home/shabir/Topo_EM_figs/SpTopoIV_8qmb5j5p_2xflexCTDs_model.pdb
> /home/shabir/Topo_EM_figs/SpTopoIV_8qmb5j5pq_on_4i3h.pdb
> /home/shabir/Topo_EM_figs/pinwheel_J238_Zflip_rsr26.pdb
Summary of feedback from opening /home/shabir/Topo_EM_figs/front_J479_rsr9.pdb
---
warnings | Cannot find LINK/SSBOND residue K (1 )
Cannot find LINK/SSBOND residue K (1 )
Cannot find LINK/SSBOND residue K (1 )
Chain information for T14mer_B-DNA.pdb #1
---
Chain | Description
A B | No description available
Chain information for E26mer_B-DNA.pdb #2
---
Chain | Description
A | No description available
B | No description available
Chain information for side_J484_rsr7.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
Chain information for front_J479_rsr9.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
Chain information for SpTopoIV_8qmb5j5pq_on_4i3h-rev.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
Q | No description available
Chain information for SpTopoIV_8qmb5j5p_2xflexCTDs_model.pdb #6
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
Chain information for SpTopoIV_8qmb5j5pq_on_4i3h.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
Q | No description available
Chain information for pinwheel_J238_Zflip_rsr26.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> color bynucleotide
> hide #1 models
> hide #2 models
> show #1 models
> show #2 models
> hide #1 models
> hide #2 models
> open /home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb
Summary of feedback from opening
/home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AA1 2 GLN A
18 VAL A 19 0
Start residue of secondary structure not found: SHEET 2 AA1 2 ALA B 105 GLY B
106 -1
Start residue of secondary structure not found: SHEET 1 AA2 3 LYS A 155 PRO A
156 0
Start residue of secondary structure not found: SHEET 2 AA2 3 ALA A 144 GLU A
151 -1
Start residue of secondary structure not found: SHEET 3 AA2 3 LYS A 161 THR A
165 -1
69 messages similar to the above omitted
Chain information for T14merA_pinwheel_5J5Q.pdb #9
---
Chain | Description
E F | No description available
> color #5,7-9#!3-4,6 bynucleotide
> hide #!3 models
> color #5,7-9#!4,6 bynucleotide
> select #9
603 atoms, 673 bonds, 29 residues, 1 model selected
> hide #!4 models
> hide #5 models
> hide #!6 models
> hide #7 models
> hide #8 models
> show sel surfaces
> ~select #9
2 models selected
> show #8 models
> select #9
603 atoms, 673 bonds, 29 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,-3.0993,0,1,0,-4.6498,0,0,1,-7.3089
> view matrix models #9,1,0,0,-5.2235,0,1,0,-6.0613,0,0,1,-6.1341
> view matrix models #9,1,0,0,-6.3816,0,1,0,-6.1306,0,0,1,-7.8567
> view matrix models #9,1,0,0,-2.9224,0,1,0,-22.22,0,0,1,-0.21635
> view matrix models #9,1,0,0,-1.8316,0,1,0,-22.573,0,0,1,-0.033346
> view matrix models #9,1,0,0,-1.9487,0,1,0,-23.809,0,0,1,-0.81871
> view matrix models #9,1,0,0,-2.0034,0,1,0,-23.645,0,0,1,-0.32886
> view matrix models #9,1,0,0,-3.0617,0,1,0,-23.635,0,0,1,0.14824
> view matrix models #9,1,0,0,-2.7272,0,1,0,-26.233,0,0,1,2.4442
> view matrix models #9,1,0,0,-1.3285,0,1,0,-25.35,0,0,1,-0.22106
> view matrix models #9,1,0,0,-2.6177,0,1,0,-25.301,0,0,1,-1.0128
> view matrix models #9,1,0,0,-2.4201,0,1,0,-25.366,0,0,1,-0.53708
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.9986,0.003658,0.052837,-14.464,-0.0057742,0.99918,0.039956,-33.095,-0.052647,-0.040205,0.9978,15.379
> view matrix models
> #9,0.98934,0.096137,0.1094,-40.703,-0.10879,0.98724,0.11631,-30.806,-0.096826,-0.12697,0.98717,39.438
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.98934,0.096137,0.1094,-39.1,-0.10879,0.98724,0.11631,-30.75,-0.096826,-0.12697,0.98717,42.508
> view matrix models
> #9,0.98934,0.096137,0.1094,-43.187,-0.10879,0.98724,0.11631,-29.912,-0.096826,-0.12697,0.98717,42.162
> view matrix models
> #9,0.98934,0.096137,0.1094,-43.175,-0.10879,0.98724,0.11631,-29.75,-0.096826,-0.12697,0.98717,42.719
> view matrix models
> #9,0.98934,0.096137,0.1094,-42.882,-0.10879,0.98724,0.11631,-29.592,-0.096826,-0.12697,0.98717,42.873
> ~select #9
2 models selected
> ui tool show "2D Builder"
Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
> ui tool show "Build Structure"
> build start nucleic T56mer_BDNA
> GCATATATATATGCGGTACGTGCGGATTGCGCTTAGACGTATGCAGGGATCGTACGA type dna form B
Chain information for T56mer_BDNA #10
---
Chain | Description
A | No description available
B | No description available
> build start nucleic T72mer_BDNA
> GCATATATATATGCGGTACGTGCGGATTGCGCTTAGACGTATGCAGGGATCGTACGATGACGATTGCATTACG
> type dna form B
Chain information for T72mer_BDNA #11
---
Chain | Description
A | No description available
B | No description available
> save /home/shabir/Topos_CTD/T56mer_BDNA.pdb models #10
> save /home/shabir/Topos_CTD/T72mer_BDNA.pdb models #11
> open /home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb
Summary of feedback from opening
/home/shabir/Topos_CTD/T14merA_pinwheel_5J5Q.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 AA1 2 GLN A
18 VAL A 19 0
Start residue of secondary structure not found: SHEET 2 AA1 2 ALA B 105 GLY B
106 -1
Start residue of secondary structure not found: SHEET 1 AA2 3 LYS A 155 PRO A
156 0
Start residue of secondary structure not found: SHEET 2 AA2 3 ALA A 144 GLU A
151 -1
Start residue of secondary structure not found: SHEET 3 AA2 3 LYS A 161 THR A
165 -1
69 messages similar to the above omitted
Chain information for T14merA_pinwheel_5J5Q.pdb #12
---
Chain | Description
E F | No description available
> hide #!9 models
> show #!9 models
> show #1 models
> coulombic #1,8,10-12#!9
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
T14mer_B-DNA.pdb #1/B C 13
T14mer_B-DNA.pdb #1/B C 13
T14mer_B-DNA.pdb #1/B G 13
T14mer_B-DNA.pdb #1/B A 13
T14mer_B-DNA.pdb #1/B A 13
T14mer_B-DNA.pdb #1/B A 13
T14mer_B-DNA.pdb #1/B A 13
T14mer_B-DNA.pdb #1/B A 13
T14mer_B-DNA.pdb #1/B G 13
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 4
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 20
pinwheel_J238_Zflip_rsr26.pdb #8/C MET 90
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 154
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 160
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 167
pinwheel_J238_Zflip_rsr26.pdb #8/C SER 168
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 205
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 225
pinwheel_J238_Zflip_rsr26.pdb #8/C ASP 238
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 240
pinwheel_J238_Zflip_rsr26.pdb #8/C ASN 253
pinwheel_J238_Zflip_rsr26.pdb #8/C GLN 256
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 296
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 311
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 313
pinwheel_J238_Zflip_rsr26.pdb #8/C ARG 353
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 370
pinwheel_J238_Zflip_rsr26.pdb #8/C GLU 390
pinwheel_J238_Zflip_rsr26.pdb #8/C ARG 393
pinwheel_J238_Zflip_rsr26.pdb #8/C LYS 394
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 20
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 154
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 161
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 167
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 169
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 205
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 225
pinwheel_J238_Zflip_rsr26.pdb #8/D ASP 238
pinwheel_J238_Zflip_rsr26.pdb #8/D ASP 265
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 296
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 311
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 313
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 370
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 384
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 390
pinwheel_J238_Zflip_rsr26.pdb #8/D ARG 393
pinwheel_J238_Zflip_rsr26.pdb #8/D LYS 394
pinwheel_J238_Zflip_rsr26.pdb #8/D ARG 396
pinwheel_J238_Zflip_rsr26.pdb #8/D GLU 398
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B A 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B G 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B C 56
T56mer_BDNA #10/B A 56
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B G 72
T72mer_BDNA #11/B C 72
T72mer_BDNA #11/B A 72
T72mer_BDNA #11/B A 72
Deleting 5' phosphates from: copy of pinwheel_J238_Zflip_rsr26.pdb #/F DA 1,
copy of pinwheel_J238_Zflip_rsr26.pdb #/H DG 1
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 5 time(s)]Coulombic values for T14mer_B-DNA.pdb_A SES surface #1.1:
minimum, -13.70, mean -9.23, maximum -1.20
Coulombic values for T14mer_B-DNA.pdb_B SES surface #1.2: minimum, -14.76,
mean -10.13, maximum -1.83
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_A SES surface #8.1:
minimum, -21.83, mean -2.08, maximum 16.59
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_B SES surface #8.2:
minimum, -18.74, mean -1.45, maximum 14.32
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_C SES surface #8.3:
minimum, -21.76, mean -2.30, maximum 17.54
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_D SES surface #8.4:
minimum, -21.65, mean -2.29, maximum 16.87
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_E SES surface #8.5:
minimum, -18.12, mean -8.12, maximum -0.35
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_F SES surface #8.6:
minimum, -17.92, mean -8.92, maximum -1.64
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_G SES surface #8.7:
minimum, -18.45, mean -8.13, maximum -0.25
Coulombic values for pinwheel_J238_Zflip_rsr26.pdb_H SES surface #8.8:
minimum, -24.22, mean -9.01, maximum -0.72
Coulombic values for T56mer_BDNA_A SES surface #10.1: minimum, -15.64, mean
-11.45, maximum -1.73
Coulombic values for T56mer_BDNA_B SES surface #10.2: minimum, -17.54, mean
-12.81, maximum -1.84
Coulombic values for T72mer_BDNA_A SES surface #11.1: minimum, -16.08, mean
-11.67, maximum -1.13
Coulombic values for T72mer_BDNA_B SES surface #11.2: minimum, -17.71, mean
-13.05, maximum -2.59
Coulombic values for T14merA_pinwheel_5J5Q.pdb_E SES surface #12.1: minimum,
-17.38, mean -9.00, maximum -0.81
Coulombic values for T14merA_pinwheel_5J5Q.pdb_F SES surface #12.2: minimum,
-16.15, mean -8.94, maximum -0.31
Coulombic values for T14merA_pinwheel_5J5Q.pdb_E SES surface #9.1: minimum,
-17.38, mean -9.00, maximum -0.81
Coulombic values for T14merA_pinwheel_5J5Q.pdb_F SES surface #9.2: minimum,
-16.15, mean -8.94, maximum -0.31
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!11 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!9 models
> hide #!10 models
> color #!1,8,12 bynucleotide
[Repeated 1 time(s)]
> hide #!12 models
> show #!12 models
> hide #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> color #!8-9,12 bynucleotide
[Repeated 1 time(s)]
> nucleotides #!8-9,12 atoms
> style nucleic & #!8-9,12 stick
Changed 2108 atom styles
> build start nucleic T88mer_BDNA
> GCATATATATATGCGGTACGTGCGGATTGCGCTTAGACGTATGCAGGGATCGTACGATGACGATTGCATTACGATGCATATATATATGC
> type dna form B
Chain information for T88mer_BDNA #13
---
Chain | Description
A | No description available
B | No description available
> select #13
3643 atoms, 4086 bonds, 178 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,0.55824,0,1,0,-0.11646,0,0,1,6.5459
> view matrix models #13,1,0,0,-1.9729,0,1,0,1.5698,0,0,1,9.1859
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.75963,0.15233,0.63226,-93.156,-0.1701,0.98488,-0.032919,37.452,-0.62771,-0.082543,0.77406,163.43
> view matrix models
> #13,0.75106,0.18482,0.63384,-97.315,-0.20122,0.97842,-0.046866,45.942,-0.62882,-0.09234,0.77205,165.55
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.75106,0.18482,0.63384,-96.682,-0.20122,0.97842,-0.046866,45.671,-0.62882,-0.09234,0.77205,165.51
> view matrix models
> #13,0.75106,0.18482,0.63384,-100.39,-0.20122,0.97842,-0.046866,46.72,-0.62882,-0.09234,0.77205,164.69
> ~select #13
Nothing selected
> ui tool show "Build Structure"
> toolshed show
Downloading bundle MolecularDynamicsViewer-1.6-py3-none-any.whl
Bundle installation canceled
Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl
> hide #!8 models
> hide #!9 models
> hide #!12 models
> hide #13 models
> open /home/shabir/Topos_CTD/Marks_model_CTD-coot-0.pdb
> /home/shabir/Topos_CTD/Marks_model_T14-72mer_G-E18mer-coot-1.pdb
Chain information for Marks_model_CTD-coot-0.pdb #14
---
Chain | Description
A | No description available
Chain information for Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J L | No description available
M | No description available
N | No description available
P | No description available
Q | No description available
> coulombic #14-15
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 4
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 20
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C MET 90
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 154
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 160
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 167
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C SER 168
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 205
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 225
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASP 238
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 240
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASN 253
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLN 256
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 296
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 311
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 313
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 353
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 370
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 390
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 393
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 394
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 20
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 154
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 161
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 167
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 169
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 205
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 225
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 238
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 265
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 296
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 311
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 313
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 370
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 384
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 390
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 393
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 394
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 396
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 398
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 9
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 10
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 11
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 12
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 13
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 14
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 15
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 16
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 17
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 18
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 2
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 3
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 4
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 5
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 6
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 7
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 8
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 9
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 10
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 11
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 12
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q G 72
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q A 72
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q C 72
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut
self.run_shortcut(keys)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut
sc.run(self.session, status = self._enabled)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run
f(s)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip
func(cmd + " %s")(session)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command
run(session, cmd)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run
run_command(session, command, **kw)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 80, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 169, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 249, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 603, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
TypeError: acc_phi_psi() takes 8 positional arguments but 46 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 46 were given
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 603, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
See log for complete Python traceback.
> select #14
2598 atoms, 2638 bonds, 326 residues, 1 model selected
> select #15
25776 atoms, 27744 bonds, 2816 residues, 1 model selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 4
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 20
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C MET 90
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 154
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 160
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 167
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C SER 168
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 205
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 225
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASP 238
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 240
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ASN 253
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLN 256
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 296
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 311
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 313
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 353
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 370
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C GLU 390
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C ARG 393
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/C LYS 394
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 20
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 154
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 161
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 167
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 169
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 205
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 225
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 238
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ASP 265
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 296
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 311
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 313
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 370
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 384
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 390
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 393
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D LYS 394
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D ARG 396
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/D GLU 398
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 9
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 10
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 11
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 12
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 13
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 14
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DC 15
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DA 16
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DT 17
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/M DG 18
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 2
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 3
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 4
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 5
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 6
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DT 7
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 8
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DG 9
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 10
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DC 11
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/N DA 12
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q G 72
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q A 72
Marks_model_T14-72mer_G-E18mer-coot-1.pdb #15/Q C 72
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut
self.run_shortcut(keys)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut
sc.run(self.session, status = self._enabled)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run
f(s)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip
func(cmd + " %s")(session)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command
run(session, cmd)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run
run_command(session, command, **kw)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 80, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 169, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 249, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 574, in find_hbonds
donor_hyds = hyd_positions(donor_atom)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> select #14
2598 atoms, 2638 bonds, 326 residues, 1 model selected
> ~select #15
2598 atoms, 2638 bonds, 326 residues, 1 model selected
OpenGL version: 3.3.0 NVIDIA 440.64
OpenGL renderer: GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Stream 8
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 78Gi 32Gi 27Gi 4.2Gi 18Gi 41Gi
Swap: 7.9Gi 0B 7.9Gi
Graphics:
09:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)
Subsystem: eVga.com. Corp. Device [3842:3081]
Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
argcomplete: 3.6.0
attrs: 25.3.0
Babel: 2.9.1
backcall: 0.2.0
basis-set-exchange: 0.11
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.30.2
ChimeraX-AtomicLibrary: 4.1.5
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3rc202111090815
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-Phenix: 0.3
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-TestManager: 0.3
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
flake8: 4.0.1
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jsonschema: 4.23.0
jsonschema-specifications: 2024.10.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
mccabe: 0.6.1
MolecularDynamicsViewer: 1.6
msgpack: 1.0.2
mypy: 0.910
mypy-extensions: 0.4.3
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.2
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 22.1.2
pkginfo: 1.7.1
prompt-toolkit: 3.0.22
psutil: 5.8.0
ptyprocess: 0.7.0
pycodestyle: 2.8.0
pycollada: 0.7.1
pydicom: 2.1.2
pydocstyle: 6.1.1
pyflakes: 2.4.0
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
referencing: 0.36.2
regex: 2024.11.6
requests: 2.26.0
rpds-py: 0.23.1
scipy: 1.7.1
Send2Trash: 1.8.0
SEQCROW: 1.6.3
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
toml: 0.10.2
tornado: 6.1
traitlets: 5.1.1
typing-extensions: 4.12.2
Unidecode: 1.3.8
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (6)
comment:1 by , 3 days ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → H-Bonds: More than 2 coplanar positions specified |
comment:2 by , 3 days ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 3 days ago
Dear Eric,
Thank you very much for getting back to me. I really appreciate you taking the time to do so. I didnt realise I was running such an old version of ChimeraX.
I just tried to upgrade to the latest version and have discovered that the problem is deeper. I am still running my linux on the old CentOS 08 system, which is no longer supported and needs to be upgraded to the latest version. The colleague who used to help me with this and to maintain everything (now I realised the amount of work he was doing) is no longer with us. He has moved to fresher pastures.
The plus side is now I've upgraded ChimeraX to latest version on my laptop and I can use this until I get someone to help me upgrade the OS on my work station.
Thanks a million.
Cheers
Shabir
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 01 December 2025 22:48
To: Shabir Najmudin <shabir.najmudin@kcl.ac.uk>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #19460: H-Bonds: More than 2 coplanar positions specified
#19460: H-Bonds: More than 2 coplanar positions specified
-----------------------------------------+----------------------------
Reporter: shabir.najmudin@… | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Analysis | Version:
Resolution: can't reproduce | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+----------------------------
Changes (by Eric Pettersen):
* resolution: => can't reproduce
* status: accepted => closed
Comment:
Hi Shabir,
We don't really have the capability to diagnose problems in 4
-year-old versions of ChimeraX. I suggest you upgrade to a current
version of ChimeraX. There is a definite chance that the problem you are
reporting has been fixed in the last 4 years. If not, please feel free to
report the problem again.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19460%23comment%3A2&data=05%7C02%7Cshabir.najmudin%40kcl.ac.uk%7C4e49d5c4328b4f5cf98e08de312bc235%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C639002261184585132%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=D%2F95YAs1FW%2Bympzv9sbmrSz3k5Mz%2FKi6x5uEYCK9S1I%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19460#comment:2>>
ChimeraX <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Cshabir.najmudin%40kcl.ac.uk%7C4e49d5c4328b4f5cf98e08de312bc235%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C639002261184611564%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=wWB%2FhRgaR5EJx17oofqFPYe8CqGwGhq1MGtQMimKUuI%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
ChimeraX Issue Tracker
comment:4 by , 3 days ago
I hope things work with the newer version. If not, feel free to submit another bug report.
--Eric
comment:5 by , 43 hours ago
Thanks Eric,
all good so far with the latest ChimeraX on my labtop!
Cheers
Shabir
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 02 December 2025 18:26
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Shabir Najmudin <shabir.najmudin@kcl.ac.uk>
Subject: Re: [ChimeraX] #19460: H-Bonds: More than 2 coplanar positions specified
#19460: H-Bonds: More than 2 coplanar positions specified
-----------------------------------------+----------------------------
Reporter: shabir.najmudin@… | Owner: Eric Pettersen
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Analysis | Version:
Resolution: can't reproduce | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+----------------------------
Comment (by Eric Pettersen):
I hope things work with the newer version. If not, feel free to submit
another bug report.
--Eric
--
Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19460%23comment%3A4&data=05%7C02%7Cshabir.najmudin%40kcl.ac.uk%7Cec4b19b84fdc46e8480508de31d05d15%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C639002968152482700%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=2VHkcyE38IiS6GmHCYdX2OOJdFYtplmsYgBpSq64E%2BI%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19460#comment:4>>
ChimeraX <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Cshabir.najmudin%40kcl.ac.uk%7Cec4b19b84fdc46e8480508de31d05d15%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C639002968152504084%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=emHdWrnEye9H5HjcglzWUMWlCQirLcDgeiBy25h4lVg%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
ChimeraX Issue Tracker
Note:
See TracTickets
for help on using tickets.
Hi Shabir,
--Eric