'CategorizedOptionsPanel' object has no attribute 'currentIndex'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.10rc202506130232 (2025-06-13 02:32:35 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202506130232 (2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:\Users\SPECTRE\Documents\Cromerix\In silico
> Analysis\APTCAD\Truncated kdo\Truncated_kdo_1_09072025\CrimeraX Session.cxs"
> format session

Log from Wed Jul 9 18:36:12 2025UCSF ChimeraX version: 1.10rc202506130232
(2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:\Users\SPECTRE\Documents\Cromerix\In silico
> Analysis\APTCAD\Dock_001_19062025\CrimeraX Session.cxs" format session

Log from Mon Jun 23 09:38:20 2025UCSF ChimeraX version: 1.10rc202506130232
(2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Dock_001_19062025/out_dock001_19062025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Dock_001_19062025/out_dock001_19062025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -8.2 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and C_2  
  
Ignored bad PDB record found on line 7  
REMARK 2 A between atoms: C_1 and O_337  
  
2182 messages similar to the above omitted  
  
Opened out_dock001_19062025.pdbqt containing 9 structures (3159 atoms, 3312
bonds)  

> viewdockx #1.1-9

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> select add #1.6

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> select add #1.7

2106 atoms, 2208 bonds, 6 residues, 6 models selected  

> select add #1.8

2457 atoms, 2576 bonds, 7 residues, 7 models selected  

> select add #1.9

2808 atoms, 2944 bonds, 8 residues, 8 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Dock_001_19062025/kdo_aptamer_model1.pdbqt"

Chain information for kdo_aptamer_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened kdo_aptamer_model1.pdbqt containing 1 structures (1845 atoms, 2022
bonds)  
Computing secondary structure  
Alignment identifier is 2/A  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1629  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1629  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1629  

> ui tool show Contacts

> contacts intraModel false intraMol false

189 contacts  

> contacts intraModel false intraMol false

189 contacts  

> hbonds sel reveal true

84 hydrogen bonds found  

> color #4 #55007fff models

> select add #4

650 atoms, 84 pseudobonds, 25 residues, 2 models selected  

> select subtract #4

650 atoms, 25 residues, 1 model selected  

> hide #3 models

> select add #4

650 atoms, 84 pseudobonds, 25 residues, 2 models selected  

> select subtract #4

650 atoms, 25 residues, 1 model selected  

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> show #4 target m

[Repeated 3 time(s)]

> select add #4

650 atoms, 84 pseudobonds, 25 residues, 2 models selected  

> select subtract #4

650 atoms, 25 residues, 1 model selected  

> select add #4

650 atoms, 84 pseudobonds, 25 residues, 2 models selected  

> select subtract #4

650 atoms, 25 residues, 1 model selected  

> hbonds sel reveal true

84 hydrogen bonds found  

> hbonds sel reveal true

84 hydrogen bonds found  

> ~hbonds

> hbonds sel reveal true

84 hydrogen bonds found  

> show #3 models

> hide #3 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> ui windowfill toggle

[Repeated 1 time(s)]

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Dock_001_19062025/out.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Dock_001_19062025/out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -18.5 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK 0 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 174  
ROOT  
  
Ignored bad PDB record found on line 526  
ENDROOT  
  
25 messages similar to the above omitted  
  
Opened out.pdbqt containing 5 structures (1755 atoms, 1840 bonds)  

> viewdockx #1.1-5

> select add #1.1

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select subtract #1.1

Nothing selected  

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> hide #1.1 models

> show #1.1 models

> select add #1.1

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #1.1 models

> select subtract #1.1

1404 atoms, 1472 bonds, 4 residues, 4 models selected  
No visible models!  

> hide #1.2 models

> hide #1.3 models

> hide #1.4 models

> hide #1.5 models

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Dock_001_19062025/out_dock001_19062025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Dock_001_19062025/out_dock001_19062025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -8.2 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and C_2  
  
Ignored bad PDB record found on line 7  
REMARK 2 A between atoms: C_1 and O_337  
  
2182 messages similar to the above omitted  
  
Opened out_dock001_19062025.pdbqt containing 9 structures (3159 atoms, 3312
bonds)  

> viewdockx #1.1-9

> select add #1.1

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select subtract #1.1

Nothing selected  

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> select add #1.6

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> select add #1.7

2106 atoms, 2208 bonds, 6 residues, 6 models selected  

> select add #1.8

2457 atoms, 2576 bonds, 7 residues, 7 models selected  

> select add #1.9

2808 atoms, 2944 bonds, 8 residues, 8 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Dock_001_19062025/kdo_aptamer_model1.pdbqt"

Chain information for kdo_aptamer_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened kdo_aptamer_model1.pdbqt containing 1 structures (1845 atoms, 2022
bonds)  
Computing secondary structure  
Alignment identifier is 2/A  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1629  

> ui tool show Contacts

> contacts intraModel false intraMol false

189 contacts  

> contacts intraModel false intraMol false

189 contacts  

> hbonds sel reveal true

84 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds color #55007f radius 0.105 dashes 8 intraModel false intraMol false
> intraRes false reveal true

27 hydrogen bonds found  

> hbonds color #55007f radius 0.105 dashes 8 intraModel false intraMol false
> intraRes false reveal true

27 hydrogen bonds found  

> hide #3 models

> ui tool show H-Bonds

> hbonds color #55007f radius 1.0 dashes 8 intraModel false intraMol false
> intraRes false reveal true

27 hydrogen bonds found  

> hbonds color #55007f radius 1.0 dashes 8 intraModel false intraMol false
> intraRes false reveal true

27 hydrogen bonds found  
No structures closed  

> log metadata #1

No models had metadata

> log chains #1

> log metadata #2

The model has no metadata

> log chains #2

Chain information for kdo_aptamer_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> show target m

[Repeated 2 time(s)]

> hide #3 models

> select add #4

650 atoms, 27 pseudobonds, 25 residues, 2 models selected  

> select subtract #4

650 atoms, 25 residues, 1 model selected  

> select add #4

650 atoms, 27 pseudobonds, 25 residues, 2 models selected  

> save "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Dock_001_19062025/CrimeraX Session.cxs"

——— End of log from Mon Jun 23 09:38:20 2025 ———

> view name session-start

opened ChimeraX session  

> close session

> hide cartoons

[Repeated 1 time(s)]

> help help:quickstart

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_1_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #1.1-9

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> select add #1.6

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> select add #1.7

2106 atoms, 2208 bonds, 6 residues, 6 models selected  

> select add #1.8

2457 atoms, 2576 bonds, 7 residues, 7 models selected  

> select add #1.9

2808 atoms, 2944 bonds, 8 residues, 8 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_1_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #2.1-9

> undo

Undo failed, probably because structures have been modified.  

> select add #2

3159 atoms, 3312 bonds, 9 residues, 10 models selected  

> select subtract #2.1

2808 atoms, 2944 bonds, 8 residues, 9 models selected  

> select add #2

3159 atoms, 3312 bonds, 9 residues, 10 models selected  

> delete atoms sel

> delete bonds sel

> delete atoms

> delete bonds

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_1_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #1.1-9

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1

3159 atoms, 3312 bonds, 9 residues, 10 models selected  

> select subtract #1

Nothing selected  

> select add #1.1

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1

3159 atoms, 3312 bonds, 9 residues, 10 models selected  

> select subtract #1.1

2808 atoms, 2944 bonds, 8 residues, 9 models selected  

> select add #1

3159 atoms, 3312 bonds, 9 residues, 10 models selected  

> select subtract #1

Nothing selected  

> select add #1

3159 atoms, 3312 bonds, 9 residues, 10 models selected  

> select subtract #1.1

2808 atoms, 2944 bonds, 8 residues, 9 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/Truncated_kdo_1_model1.pdbqt"

Chain information for Truncated_kdo_1_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened Truncated_kdo_1_model1.pdbqt containing 1 structures (805 atoms, 882
bonds)  
Computing secondary structure  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1473  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1473  

> ui tool show Contacts

> contacts sel intraModel false intraMol false select true radius 0.095

No atoms match given atom specifier  

> contacts sel intraModel false intraMol false select true radius 0.095

No atoms match given atom specifier  

> contacts sel intraModel false intraMol false select true radius 0.095

No atoms match given atom specifier  
Alignment identifier is 2/A  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> ui tool show H-Bonds

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

24 hydrogen bonds found  

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

24 hydrogen bonds found  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_1_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #1.1-9

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> select add #1.6

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> select add #1.7

2106 atoms, 2208 bonds, 6 residues, 6 models selected  

> select add #1.8

2457 atoms, 2576 bonds, 7 residues, 7 models selected  

> select add #1.9

2808 atoms, 2944 bonds, 8 residues, 8 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/Truncated_kdo_1_model1.pdbqt"

Chain information for Truncated_kdo_1_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened Truncated_kdo_1_model1.pdbqt containing 1 structures (805 atoms, 882
bonds)  
Computing secondary structure  
Alignment identifier is 2/A  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1473  

> ui tool show Contacts

> contacts sel intraModel false intraMol false select true radius 0.095

No atoms match given atom specifier  

> contacts sel intraModel false intraMol false select true radius 0.095

196 contacts  

> contacts sel intraModel false intraMol false select true radius 0.095

196 contacts  

> ui tool show H-Bonds

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

24 hydrogen bonds found  

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

24 hydrogen bonds found  

> save "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated kdo/Truncated_kdo_1_09072025/CrimeraX Session.cxs"

——— End of log from Wed Jul 9 18:36:12 2025 ———

> view name session-start

opened ChimeraX session  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_1_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #5.1-9

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_1_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #1.1-9

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> select add #1.6

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> select add #1.7

2106 atoms, 2208 bonds, 6 residues, 6 models selected  

> select add #1.8

2457 atoms, 2576 bonds, 7 residues, 7 models selected  

> select add #1.9

2808 atoms, 2944 bonds, 8 residues, 8 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/Truncated_kdo_1_model1.pdbqt"

Chain information for Truncated_kdo_1_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened Truncated_kdo_1_model1.pdbqt containing 1 structures (805 atoms, 882
bonds)  
Computing secondary structure  
Alignment identifier is 2/A  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1473  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1473  

> ui tool show Contacts

QWindowsWindow::setGeometry: Unable to set geometry 530x754+935+338 (frame:
548x801+926+300) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 528x746+936+345 (frame: 546x793+927+307)
margins: 9, 38, 9, 9 minimum size: 424x603 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=548, y=801)))  

> contacts sel intraModel false intraMol false select true radius 0.095

196 contacts  

> contacts sel intraModel false intraMol false select true radius 0.095

196 contacts  

> color #3 #ffaa00ff models

QWindowsWindow::setGeometry: Unable to set geometry 315x125+1043+651 (frame:
333x172+1034+613) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 313x117+1044+658 (frame:
331x164+1035+620) margins: 9, 38, 9, 9 minimum size: 252x100 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=333, y=172)))  

QWindowsWindow::setGeometry: Unable to set geometry 625x316+888+556 (frame:
643x363+879+518) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 623x308+889+563 (frame: 641x355+880+525)
margins: 9, 38, 9, 9 minimum size: 500x204 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=643, y=302)))  

> view #2/A:10

> select #2/A:9

29 atoms, 31 bonds, 1 residue, 1 model selected  

> select #2/A:9

29 atoms, 31 bonds, 1 residue, 1 model selected  

QWindowsWindow::setGeometry: Unable to set geometry 483x393+959+518 (frame:
501x440+950+480) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 481x385+960+525 (frame: 499x432+951+487)
margins: 9, 38, 9, 9 minimum size: 276x206 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=363, y=305)))  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 423, in _save  
for opt in self._get_actionable_options():  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 385, in
_get_actionable_options  
options = self.options_panel.options(self.options_panel.current_category())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 251, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 251, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_1_09072025/out_truncated_kdo_1_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.0 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_1_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #1.1-9

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> select add #1.6

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> select add #1.7

2106 atoms, 2208 bonds, 6 residues, 6 models selected  

> select add #1.8

2457 atoms, 2576 bonds, 7 residues, 7 models selected  

> select add #1.9

2808 atoms, 2944 bonds, 8 residues, 8 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/Truncated_kdo_1_model1.pdbqt"

Chain information for Truncated_kdo_1_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened Truncated_kdo_1_model1.pdbqt containing 1 structures (805 atoms, 882
bonds)  
Computing secondary structure  
Alignment identifier is 2/A  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1473  

> ui tool show H-Bonds

QWindowsWindow::setGeometry: Unable to set geometry 551x650+925+389 (frame:
569x697+916+351) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 549x642+926+396 (frame: 567x689+917+358)
margins: 9, 38, 9, 9 minimum size: 441x520 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=569, y=697)))  

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

24 hydrogen bonds found  

QWindowsWindow::setGeometry: Unable to set geometry 483x393+959+518 (frame:
501x440+950+480) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 481x385+960+525 (frame: 499x432+951+487)
margins: 9, 38, 9, 9 minimum size: 276x206 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=363, y=305)))  

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

24 hydrogen bonds found  

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

24 hydrogen bonds found  

> color #3 #00aa00ff models

> color #3 #00007fff models

> color #3 #aa00ffff models

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/Truncated_kdo_1_model1.pdbqt"

Chain information for Truncated_kdo_1_model1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
Opened Truncated_kdo_1_model1.pdbqt containing 1 structures (805 atoms, 882
bonds)  

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_1_09072025/Truncated_kdo_1_model1.pdbqt"

Chain information for Truncated_kdo_1_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened Truncated_kdo_1_model1.pdbqt containing 1 structures (805 atoms, 882
bonds)  
Computing secondary structure  

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated kdo/Truncated_kdo_1_09072025/Truncated_kdo_1.pdb"

Chain information for Truncated_kdo_1.pdb #3  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated kdo/Truncated_kdo_1_09072025/Truncated_kdo_1.pdb"

Chain information for Truncated_kdo_1.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated kdo/Truncated_kdo_2_09072025/Truncated_kdo_2.pdb"

Chain information for Truncated_kdo_2.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> close session

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_2_09072025/out_truncated_kdo_2_09072025.pdbqt"

Summary of feedback from opening C:/Users/SPECTRE/Documents/Cromerix/In silico
Analysis/APTCAD/Truncated
kdo/Truncated_kdo_2_09072025/out_truncated_kdo_2_09072025.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.3 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!  
  
Ignored bad PDB record found on line 4  
REMARK 169 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: C_1 and O_337  
  
4621 messages similar to the above omitted  
  
Opened out_truncated_kdo_2_09072025.pdbqt containing 9 structures (3159 atoms,
3312 bonds)  

> viewdockx #1.1-9

> select add #1.2

351 atoms, 368 bonds, 1 residue, 1 model selected  

> select add #1.3

702 atoms, 736 bonds, 2 residues, 2 models selected  

> select add #1.4

1053 atoms, 1104 bonds, 3 residues, 3 models selected  

> select add #1.5

1404 atoms, 1472 bonds, 4 residues, 4 models selected  

> select add #1.6

1755 atoms, 1840 bonds, 5 residues, 5 models selected  

> select add #1.7

2106 atoms, 2208 bonds, 6 residues, 6 models selected  

> select add #1.8

2457 atoms, 2576 bonds, 7 residues, 7 models selected  

> select add #1.9

2808 atoms, 2944 bonds, 8 residues, 8 models selected  

> delete atoms sel

> delete bonds sel

> open "C:/Users/SPECTRE/Documents/Cromerix/In silico
> Analysis/APTCAD/Truncated
> kdo/Truncated_kdo_2_09072025/Truncated_kdo_2_model1.pdbqt"

Chain information for Truncated_kdo_2_model1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Opened Truncated_kdo_2_model1.pdbqt containing 1 structures (600 atoms, 658
bonds)  
Computing secondary structure  
Alignment identifier is 2/A  

> interfaces ~solvent

1 buried areas: #2/A #1.1/ 1429  

> hide #2 models

> show #2 models

> select add #2

600 atoms, 658 bonds, 23 residues, 1 model selected  

> select subtract #2

Nothing selected  

QWindowsWindow::setGeometry: Unable to set geometry 483x393+959+518 (frame:
501x440+950+480) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 481x385+960+525 (frame: 499x432+951+487)
margins: 9, 38, 9, 9 minimum size: 276x206 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=363, y=305)))  

> ui tool show Contacts

QWindowsWindow::setGeometry: Unable to set geometry 530x754+935+338 (frame:
548x801+926+300) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 528x746+936+345 (frame: 546x793+927+307)
margins: 9, 38, 9, 9 minimum size: 424x603 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=548, y=801)))  

> contacts sel intraModel false intraMol false select true radius 0.095

244 contacts  

> contacts sel intraModel false intraMol false select true radius 0.095

244 contacts  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> ui tool show H-Bonds

QWindowsWindow::setGeometry: Unable to set geometry 551x650+925+389 (frame:
569x697+916+351) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 549x642+926+396 (frame: 567x689+917+358)
margins: 9, 38, 9, 9 minimum size: 441x520 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=569, y=697)))  

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

31 hydrogen bonds found  

> hbonds color #55007f radius 1.0 dashes 20 intraModel false intraMol false
> intraRes false select true reveal true

31 hydrogen bonds found  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 423, in _save  
for opt in self._get_actionable_options():  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 385, in
_get_actionable_options  
options = self.options_panel.options(self.options_panel.current_category())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 251, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 251, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 423, in _save  
for opt in self._get_actionable_options():  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 385, in
_get_actionable_options  
options = self.options_panel.options(self.options_panel.current_category())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 251, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
AttributeError: 'CategorizedOptionsPanel' object has no attribute
'currentIndex'  
  
File "C:\Program Files\ChimeraX 1.10rc202506130232\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 251, in current_category  
return self._tabs_widget.tabText(self.currentIndex())  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 750x609+825+410 (frame:
768x656+816+372) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 748x601+826+417 (frame: 766x648+817+379)
margins: 9, 38, 9, 9 minimum size: 600x333 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=463)))  




OpenGL version: 3.3.0 - Build 31.0.101.2111
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: HP
Model: HP Pavilion x360 Convertible
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,482,357,248
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.4.0
    build: 1.2.2.post1
    certifi: 2025.6.15
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202506130232
    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: 1.1.4
    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: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    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-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Eric Pettersen]

Fixed on 6/20/25