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 "C:/Documentos/Sonia/Curso
> ChimeraX_2026/EjercicioExtra/Groel/emd_8750.map"

Opened emd_8750.map as #1, grid size 240,240,240, pixel 1.23, shown at level
0.0402, step 1, values float32  

> open "C:/Documentos/Sonia/Curso
> ChimeraX_2026/EjercicioExtra/Groel/5w0s_monomerA.pdb"

5w0s_monomerA.pdb title:  
Groel using cryoem [more info...]  
  
Chain information for 5w0s_monomerA.pdb #2  
---  
Chain | Description | UniProt  
A | 60 kda chaperonin | Q6Q099_ECOLX 2-525  
  

> select add #2

3870 atoms, 3879 bonds, 543 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,32.401,0,1,0,-4.2034,0,0,1,-63.295

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.93646,-0.3505,0.013596,93.168,0.098463,0.29988,0.94888,-52.033,-0.33666,-0.88725,0.31534,222.54

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,226.33,0.99603,-0.032476,-0.082906,209.91,-0.022606,-0.99284,0.11733,281.9

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,372.62,0.99603,-0.032476,-0.082906,242.94,-0.022606,-0.99284,0.11733,232.59

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,380.96,0.99603,-0.032476,-0.082906,232.4,-0.022606,-0.99284,0.11733,271.16

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,381.78,0.99603,-0.032476,-0.082906,187.71,-0.022606,-0.99284,0.11733,271.06

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,391.3,0.99603,-0.032476,-0.082906,175.98,-0.022606,-0.99284,0.11733,273.21

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,392.06,0.99603,-0.032476,-0.082906,175.29,-0.022606,-0.99284,0.11733,271.96

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,400.37,0.99603,-0.032476,-0.082906,185.19,-0.022606,-0.99284,0.11733,274.12

> select clear

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01426, steps = 88  
shifted from previous position = 1.8  
rotated from previous position = 6.27 degrees  
atoms outside contour = 3245, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
0.01606642 -0.11326973 -0.99343437 401.49776610  
0.99796578 -0.05948827 0.02292246 172.23684464  
-0.06169412 -0.99178179 0.11208355 273.69217599  
Axis -0.57330587 -0.52643137 0.62784584  
Axis point 280.60879584 352.83867193 0.00000000  
Rotation angle (degrees) 117.75353674  
Shift along axis -149.01540911  
  

> select add #2

3870 atoms, 3879 bonds, 543 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.028054,0.43842,-0.89833,283.26,0.85357,-0.47821,-0.20672,289.88,-0.52022,-0.76099,-0.38763,319.84

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.028054,0.43842,-0.89833,281.57,0.85357,-0.47821,-0.20672,288.06,-0.52022,-0.76099,-0.38763,320.8

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.028054,0.43842,-0.89833,271.99,0.85357,-0.47821,-0.20672,286.49,-0.52022,-0.76099,-0.38763,312.21

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.23373,0.73372,-0.63798,166.94,0.69099,-0.33627,-0.63989,339.52,-0.68404,-0.5904,-0.4284,286.98

> view matrix models
> #2,-0.4608,0.84252,-0.27898,77.933,0.45205,-0.047703,-0.89072,331.08,-0.76375,-0.53656,-0.35888,263.39

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01777, steps = 116  
shifted from previous position = 3.91  
rotated from previous position = 12.7 degrees  
atoms outside contour = 3098, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.53383562 0.74403247 -0.40179002 118.19507626  
0.58297715 -0.02033986 -0.81223392 314.19580887  
-0.61250076 -0.66783379 -0.42289579 304.63717083  
Axis 0.47818483 0.69777419 -0.53333896  
Axis point -28.69975753 0.00000000 268.91180194  
Rotation angle (degrees) 171.31582617  
Shift along axis 113.28194823  
  

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01777, steps = 48  
shifted from previous position = 0.00321  
rotated from previous position = 0.00712 degrees  
atoms outside contour = 3098, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.53393407 0.74396549 -0.40178322 118.20407305  
0.58296564 -0.02027077 -0.81224391 314.18705575  
-0.61242589 -0.66791051 -0.42288306 304.65184338  
Axis 0.47813643 0.69780062 -0.53334777  
Axis point -28.68472024 0.00000000 268.91359090  
Rotation angle (degrees) 171.31898471  
Shift along axis 113.27221771  
  

> select clear

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01777, steps = 60  
shifted from previous position = 0.0198  
rotated from previous position = 0.0294 degrees  
atoms outside contour = 3097, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.53385021 0.74401227 -0.40180805 118.19585852  
0.58269374 -0.02065750 -0.81242924 314.28420126  
-0.61275767 -0.66784655 -0.42250328 304.54798237  
Axis 0.47816493 0.69765414 -0.53351381  
Axis point -28.71734716 0.00000000 268.95609821  
Rotation angle (degrees) 171.30439704  
Shift along axis 113.29823517  
  

> transparency 50

> ui mousemode right "translate selected models"

> select add #2

3870 atoms, 3879 bonds, 543 residues, 1 model selected  

> view matrix models
> #2,-0.53385,0.74401,-0.40181,119.61,0.58269,-0.020658,-0.81243,316.45,-0.61276,-0.66785,-0.4225,302.55

> view matrix models
> #2,-0.53385,0.74401,-0.40181,155.35,0.58269,-0.020658,-0.81243,376.56,-0.61276,-0.66785,-0.4225,318.52

> view matrix models
> #2,-0.53385,0.74401,-0.40181,141.21,0.58269,-0.020658,-0.81243,351.18,-0.61276,-0.66785,-0.4225,309.96

> view matrix models
> #2,-0.53385,0.74401,-0.40181,141.81,0.58269,-0.020658,-0.81243,348.23,-0.61276,-0.66785,-0.4225,301.14

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.59355,0.63071,-0.4999,180.12,0.47521,-0.22664,-0.85018,391.73,-0.64952,-0.74218,-0.16519,266.44

> view matrix models
> #2,-0.61875,0.50352,-0.603,222.25,0.6016,-0.18991,-0.77589,372.51,-0.50519,-0.84285,-0.18542,290.06

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.61875,0.50352,-0.603,225.02,0.6016,-0.18991,-0.77589,387.82,-0.50519,-0.84285,-0.18542,315.4

> view matrix models
> #2,-0.61875,0.50352,-0.603,201.79,0.6016,-0.18991,-0.77589,343.17,-0.50519,-0.84285,-0.18542,294.63

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.05266, steps = 80  
shifted from previous position = 5.27  
rotated from previous position = 8.09 degrees  
atoms outside contour = 1603, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.62786285 0.39081539 -0.67309106 238.56749641  
0.66540920 -0.17908472 -0.72467873 328.84863044  
-0.40375593 -0.90287983 -0.14761152 301.81944619  
Axis -0.42037588 -0.63536080 0.64776599  
Axis point 195.98712664 328.22817834 0.00000000  
Rotation angle (degrees) 167.76308568  
Shift along axis -113.71717867  
  

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.05266, steps = 60  
shifted from previous position = 0.0195  
rotated from previous position = 0.0344 degrees  
atoms outside contour = 1610, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.62771733 0.39092638 -0.67316233 238.57161894  
0.66526053 -0.17964756 -0.72467591 328.93878596  
-0.40422690 -0.90271996 -0.14730000 301.71479671  
Axis -0.42048960 -0.63514932 0.64789956  
Axis point 195.98378971 328.11807717 -0.00000000  
Rotation angle (degrees) 167.77739501  
Shift along axis -113.76124344  
  

> select clear

> sym #2 symetry #1

Expected a keyword  

> sym #2 symmetry #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\sym.py", line 100, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 510, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 520, in parse_symmetry  
ops = ops * group_symmetries(session, g, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in group_symmetries  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in <listcomp>  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> sym #2 symmetry #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\sym.py", line 100, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 510, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 520, in parse_symmetry  
ops = ops * group_symmetries(session, g, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in group_symmetries  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in <listcomp>  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
  
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)))  

> volume #1 level 0.04185




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

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

Manufacturer: LENOVO
Model: 81WE
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 8,319,787,008
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G1 CPU @ 1.00GHz
OSLanguage: es-ES

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
    babel: 2.17.0
    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-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
    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
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    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
    msgpack: 1.1.1
    multidict: 6.7.0
    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: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    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
    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
    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
    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
    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
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0