ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "U:/KARAN_POSTDOC_DATA/EXO1_PROJECT/XL-MS Exo1-PCNA/PDB/PCNA-MBP-EXO1
> 301-402_fold_2026_05_20_17_33.zip"

Unrecognized file suffix '.zip'  

> open "U:/KARAN_POSTDOC_DATA/EXO1_PROJECT/XL-MS Exo1-PCNA/PDB/PCNA-MBP-EXO1
> 301-402_fold_2026_05_20_17_33/fold_2026_05_20_17_33_model_0.cif"

Chain information for fold_2026_05_20_17_33_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> select /B:1-279

2188 atoms, 2225 bonds, 279 residues, 1 model selected  

> color sel red

> hide #1 models

> close

> close #

Expected a models specifier or a keyword  

> open "U:/KARAN_POSTDOC_DATA/EXO1_PROJECT/XL-MS
> Exo1-PCNA/PDB/POL30-P15873-F1-model_v6.pdb"

POL30-P15873-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for proliferating cell nuclear antigen
(P15873) [more info...]  
  
Chain information for POL30-P15873-F1-model_v6.pdb #1  
---  
Chain | Description | UniProt  
A | proliferating cell nuclear antigen | PCNA_YEAST 1-258  
  
Computing secondary structure  

> show target m

> view clip false

[Repeated 1 time(s)]

> color red

> log metadata #1

Metadata for POL30-P15873-F1-model_v6.pdb #1  
---  
Title | Alphafold monomer V2.0 prediction for proliferating cell nuclear antigen (P15873)  
Source (natural) | Saccharomyces cerevisiae (strain ATCC 204508 / S288C)  
  
> log chains #1

Chain information for POL30-P15873-F1-model_v6.pdb #1  
---  
Chain | Description | UniProt  
A | proliferating cell nuclear antigen | PCNA_YEAST 1-258  
  

> view clip false

> show target m

> hide target m

[Repeated 1 time(s)]

> show target m

> open "U:/KARAN_POSTDOC_DATA/EXO1_PROJECT/XL-MS Exo1-PCNA/PDB/MBP-EXO1
> 301-402-fold_2026_05_20_17_17/fold_2026_05_20_17_17_model_0.cif"

Chain information for fold_2026_05_20_17_17_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> hide #2 models

> select add #2

3940 atoms, 4037 bonds, 500 residues, 1 model selected  

> close #2

> open "U:/KARAN_POSTDOC_DATA/EXO1_PROJECT/XL-MS Exo1-PCNA/PDB/MBP-EXO1
> 301-402-fold_2026_05_20_17_17/fold_2026_05_20_17_17_model_0.cif"

Chain information for fold_2026_05_20_17_17_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui mousemode right "translate selected models"

[Repeated 7 time(s)]

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,-1.7935,0,1,0,-45.489,0,0,1,47.089

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,48.921,0,1,0,-22.077,0,0,1,52.333

> view matrix models #1,1,0,0,-28.423,0,1,0,-20.018,0,0,1,19.004

> view matrix models #1,1,0,0,-26.91,0,1,0,-19.357,0,0,1,18.742

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-24.499,0,1,0,-9.7154,0,0,1,9.2735

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

[Repeated 4 time(s)]

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,50.225,0,1,0,-7.0499,0,0,1,41.547

> ui mousemode right "move picked models"

[Repeated 1 time(s)]

> view matrix models #2,1,0,0,37.634,0,1,0,-9.591,0,0,1,38.794

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:500

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:401-500

827 atoms, 844 bonds, 100 residues, 1 model selected  

> color sel purple

> select #2/A:365

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:493

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2/A:492-493

22 atoms, 23 bonds, 2 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:258

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #1/A:257-258

19 atoms, 18 bonds, 2 residues, 1 model selected  

> color sel yellow

> select #1/A:189

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:188-189

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #2/A:455

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:453-455

30 atoms, 31 bonds, 3 residues, 1 model selected  

> color sel lime

> select #1/A:10

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/A:10-15

53 atoms, 53 bonds, 6 residues, 1 model selected  

> select
> #1/A:2-6,25-31,34-40,46-53,59-62,66-71,87-92,98-105,110-117,135-140,157-162,167-173,176-182,196-199,203-208,224-229,235-240,244-250

886 atoms, 881 bonds, 114 residues, 1 model selected  

> select #1/A:13

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:13-14

20 atoms, 19 bonds, 2 residues, 1 model selected  

> color sel lime

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-19.726,0,1,0,-10.259,0,0,1,10.086

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.72283,-0.32407,-0.61033,-21.336,0.68562,0.44659,0.57487,-9.5038,0.086271,-0.83399,0.54499,8.3605

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,16.16,0,1,0,-8.2794,0,0,1,22.108

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.72283,-0.32407,-0.61033,-26.168,0.68562,0.44659,0.57487,-5.3764,0.086271,-0.83399,0.54499,-3.593

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.70755,-0.29878,-0.64039,-26.218,0.67402,0.55756,0.48458,-5.5179,0.21228,-0.7745,0.59589,-3.4786

> view matrix models
> #1,0.81214,-0.012376,-0.58333,-25.925,0.4739,0.59721,0.64712,-5.009,0.34036,-0.80199,0.49088,-3.8083

> view matrix models
> #1,0.7556,-0.039628,-0.65383,-26.094,0.53444,0.61443,0.58039,-5.1862,0.37873,-0.78798,0.48544,-3.8278

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.7556,-0.039628,-0.65383,3.0749,0.53444,0.61443,0.58039,-9.2391,0.37873,-0.78798,0.48544,23.697

> ui mousemode right "move planes"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.7556,-0.039628,-0.65383,-15.093,0.53444,0.61443,0.58039,1.5492,0.37873,-0.78798,0.48544,-11.603

> ui mousemode right "move planes"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.7556,-0.039628,-0.65383,-24.475,0.53444,0.61443,0.58039,7.9451,0.37873,-0.78798,0.48544,-15.754

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.62423,0.073959,-0.77773,-24.649,0.55724,0.65559,0.5096,7.7897,0.54756,-0.75149,0.36802,-16.087

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.62423,0.073959,-0.77773,-29.019,0.55724,0.65559,0.5096,13.152,0.54756,-0.75149,0.36802,-18.639

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.62423,0.073959,-0.77773,-29.008,0.55724,0.65559,0.5096,12.972,0.54756,-0.75149,0.36802,-18.395

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.62423,0.073959,-0.77773,-28.15,0.55724,0.65559,0.5096,14.277,0.54756,-0.75149,0.36802,-20.108

> ui mousemode right "translate selected models"

> select #2/A:47

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/A:47

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-2.5687,0,1,0,6.7896,0,0,1,-12.425

> ui mousemode right "move picked models"

> select #2/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:1-400

3113 atoms, 3192 bonds, 400 residues, 1 model selected  

> delete ~ sel

> select clear

[Repeated 1 time(s)]

> delete ~ sel

> toolshed show

Installed ChimeraX-XMAS (1.1.3)  

> ui tool show XMAS

> open "U:/KARAN_POSTDOC_DATA/EXO1_PROJECT/XL-MS Exo1-PCNA/PDB/MBP-EXO1
> 301-402-fold_2026_05_20_17_17/fold_2026_05_20_17_17_model_0.cif"

Chain information for fold_2026_05_20_17_17_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> view matrix models #1,1,0,0,-25.291,0,1,0,-2.7929,0,0,1,0

> color red

> color lime

> color cornflower blue

> open "U:/KARAN_POSTDOC_DATA/EXO1_PROJECT/XL-MS
> Exo1-PCNA/PDB/POL30-P15873-F1-model_v6.pdb"

POL30-P15873-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for proliferating cell nuclear antigen
(P15873) [more info...]  
  
Chain information for POL30-P15873-F1-model_v6.pdb #2  
---  
Chain | Description | UniProt  
A | proliferating cell nuclear antigen | PCNA_YEAST 1-258  
  
Computing secondary structure  

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,1.1333,0,1,0,-1.0271,0,0,1,0.030862

> view matrix models #2,1,0,0,21.127,0,1,0,-39.259,0,0,1,10.487

> ui tool show XMAS

Please select pseudobonds  
Unsupported evidence file format  
Traceback (most recent call last):  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Unsupported evidence file format  
Traceback (most recent call last):  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Unsupported evidence file format  
Traceback (most recent call last):  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Please check one or more files  
Unsupported evidence file format  
Traceback (most recent call last):  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Please select pseudobonds  
Please select pseudobonds  
Traceback (most recent call last):  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\pandas\core\indexes\base.py", line 3641, in get_loc  
return self._engine.get_loc(casted_key)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "pandas/_libs/index.pyx", line 168, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/index.pyx", line 197, in
pandas._libs.index.IndexEngine.get_loc  
File "pandas/_libs/hashtable_class_helper.pxi", line 7668, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
File "pandas/_libs/hashtable_class_helper.pxi", line 7676, in
pandas._libs.hashtable.PyObjectHashTable.get_item  
KeyError: 'PSMID'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 105, in __init__  
self.engines[engine][1](df)  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 131, in
parse_xlinkx_xi_seqs_scores  
function(peptide_pairs, df, xi_alternative)  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\XMAS\read_evidence.py", line 218, in parse_xi_pos_ids  
params[key] = df[col_name].tolist()  
~~^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\pandas\core\frame.py", line 4378, in __getitem__  
indexer = self.columns.get_loc(key)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\pandas\core\indexes\base.py", line 3648, in get_loc  
raise KeyError(key) from err  
KeyError: 'PSMID'  
  
KeyError: 'PSMID'  
  
File "C:\Users\choudhak\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\pandas\core\indexes\base.py", line 3648, in get_loc  
raise KeyError(key) from err  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.8247
OpenGL renderer: Intel(R) Arc(TM) 140V GPU (16GB)
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_IN.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Dell Pro 14 Plus PB14250
OS: Microsoft Windows 11 Education (Build 26200)
Memory: 33,895,956,480
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) Ultra 7 268V
OSLanguage: de-DE

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    autocommand: 2.2.2
    babel: 2.17.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    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: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    et_xmlfile: 2.0.0
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    inflect: 7.3.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jaraco.collections: 5.1.0
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    more-itertools: 10.3.0
    msgpack: 1.1.1
    multidict: 6.7.0
    narwhals: 2.16.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 2.4.2
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openpyxl: 3.1.5
    openvr: 1.26.701
    packaging: 25.0
    packaging: 24.2
    pandas: 3.0.3
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    platformdirs: 4.2.2
    plotly: 6.5.2
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.9.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    QtRangeSlider: 0.1.5
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    seaborn: 0.13.2
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomli: 2.0.1
    tomlkit: 0.14.0
    tornado: 6.5.4
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    typing_extensions: 4.12.2
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0
    zipp: 3.19.2