Opened 15 hours ago

Closed 7 hours ago

#19460 closed defect (can't reproduce)

H-Bonds: More than 2 coplanar positions specified

Reported by: shabir.najmudin@… 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 (2)

comment:1 by Eric Pettersen, 7 hours ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → H-Bonds: More than 2 coplanar positions specified

comment:2 by Eric Pettersen, 7 hours ago

Resolution: → can't reproduce
Status: accepted → closed

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

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