ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202512132024 (2025-12-13 20:24:14 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
> phenix location /Users/akrebs/Applications/phenix-2.0-5848

Using Phenix installation /Users/akrebs/Applications/phenix-2.0-5848  

> ui tool hide "command line interface"

> ui tool show clix

UCSF ChimeraX version: 1.12.dev202512132024 (2025-12-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/akrebs/Team Nicolas Thoma Dropbox/cryo-EM cryo-
> EM/KBTBD4-CoREST_structure/continue model building/May26/25_Aloop94.cif"

Summary of feedback from opening /Users/akrebs/Team Nicolas Thoma
Dropbox/cryo-EM cryo-EM/KBTBD4-CoREST_structure/continue model
building/May26/25_Aloop94.cif  
---  
warnings | Unknown polymer entity '3' on line 26103  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Atom H is not in the residue template for MET /D:59  
Atom N3 is not in the residue template for A1A /E:503  
  
Chain information for 25_Aloop94.cif #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> open "/Users/akrebs/Team Nicolas Thoma Dropbox/cryo-EM cryo-
> EM/KBTBD4-CoREST_structure/continue model
> building/May26/26_D174-204Afold.cif"

Summary of feedback from opening /Users/akrebs/Team Nicolas Thoma
Dropbox/cryo-EM cryo-EM/KBTBD4-CoREST_structure/continue model
building/May26/26_D174-204Afold.cif  
---  
warnings | Unknown polymer entity '3' on line 26103  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Atom H is not in the residue template for MET /D:59  
Atom N3 is not in the residue template for A1A /E:503  
  
Chain information for 26_D174-204Afold.cif #2  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> hide atoms

> show cartoons

> hide #!1 models

> show #!1 models

> color #2 #d4fb79ff

> color #1 #73fdffff

> select /D

9044 atoms, 9150 bonds, 2 pseudobonds, 556 residues, 4 models selected  

> select ~sel

65032 atoms, 65784 bonds, 4122 residues, 2 models selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> style sel stick

Changed 65032 atom styles  

> show sel atoms

> select /D

9044 atoms, 9150 bonds, 2 pseudobonds, 556 residues, 4 models selected  

> undo

[Repeated 1 time(s)]

> select /D

9044 atoms, 9150 bonds, 2 pseudobonds, 556 residues, 4 models selected  

> style (#!1-2 & sel) stick

Changed 9044 atom styles  

> show sel atoms

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> close #2

> close #1

> open "/Users/akrebs/Team Nicolas Thoma Dropbox/cryo-EM cryo-
> EM/KBTBD4-CoREST_structure/continue model building/May26/28_chainG.cif"

Summary of feedback from opening /Users/akrebs/Team Nicolas Thoma
Dropbox/cryo-EM cryo-EM/KBTBD4-CoREST_structure/continue model
building/May26/28_chainG.cif  
---  
warnings | Unknown polymer entity '3' on line 26103  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Atom H is not in the residue template for MET /D:59  
Atom N3 is not in the residue template for A1A /E:503  
  
Chain information for 28_chainG.cif #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> hide atoms

> hide cartoons

> show cartoons

> set bgColor white

> set bgColor black

> open "/Users/akrebs/Team Nicolas Thoma Dropbox/cryo-EM cryo-
> EM/KBTBD4-CoREST_structure/continue model
> building/April26/maps_base/cryosparc_P8_J753_map_sharp_deepemhancer.mrc"

Opened cryosparc_P8_J753_map_sharp_deepemhancer.mrc as #2, grid size
384,384,384, pixel 0.732, shown at level 0.000121, step 2, values float32  

> volume #2 level 0.0275

> volume #2 step 1

> volume #2 level 0.08835

> volume #2 level 0.07289

> open "/Users/akrebs/Team Nicolas Thoma Dropbox/cryo-EM cryo-
> EM/KBTBD4-CoREST_structure/continue model
> building/April26/maps_base/cryosparc_P8_J751_008_volume_map.mrc"

Opened cryosparc_P8_J751_008_volume_map.mrc as #3, grid size 384,384,384,
pixel 0.732, shown at level 0.0079, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.03443

> volume #2 level 0.09502

> volume #3 level 0.02913

> select #1/A:474

15 atoms, 14 bonds, 1 residue, 1 model selected  

> open "/Users/akrebs/Team Nicolas Thoma Dropbox/cryo-EM cryo-
> EM/pp2a/todeposit/full/FINAL_k4pp2a_isolde_0k_model4phenix_real_space_refined_000_mod_final.pdb"

Chain information for
FINAL_k4pp2a_isolde_0k_model4phenix_real_space_refined_000_mod_final.pdb #4  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> mmaker #4/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 28_chainG.cif, chain A (#1) with
FINAL_k4pp2a_isolde_0k_model4phenix_real_space_refined_000_mod_final.pdb,
chain A (#4), sequence alignment score = 2647.4  
RMSD between 476 pruned atom pairs is 0.716 angstroms; (across all 495 pairs:
1.170)  
  

> hide #4/C

> hide #4/C ribbons

> hide #4/D ribbons

> hide #!4 models

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.2029

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> volume #3 level 0.02488

> volume #3 level 0.03072

> volume #3 level 0.03868

> show #!4 models

> volume #3 level 0.03443

> volume #3 color #ffffb2cc

> show #1/A atoms

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1463, in register_command  
return cls._get_func(api, "register_command")(bi, ci, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/animations/__init__.py", line 35, in register_command  
cmd.register_command(ci.name, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/animations/cmd.py", line 70, in register_command  
raise ValueError("trying to register unknown command: %s" % command_name)  
ValueError: trying to register unknown command: animations  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/akrebs/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 107, in _selection_changed  
tooltip_widget.setWordInfo(winfo, text)  
File "/Users/akrebs/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 493, in setWordInfo  
cmd_desc = resolve_cmd_desc(word_info, command_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/akrebs/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/clix/_types.py", line 85, in resolve_cmd_desc  
winfo.cmd_desc.proxy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
animations in bundle ChimeraX-Animations:  
trying to register unknown command: animations  
  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
animations in bundle ChimeraX-Animations:  
trying to register unknown command: animations  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd  
raise ToolshedError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1463, in register_command  
return cls._get_func(api, "register_command")(bi, ci, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/animations/__init__.py", line 35, in register_command  
cmd.register_command(ci.name, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/animations/cmd.py", line 70, in register_command  
raise ValueError("trying to register unknown command: %s" % command_name)  
ValueError: trying to register unknown command: animations  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/akrebs/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 107, in _selection_changed  
tooltip_widget.setWordInfo(winfo, text)  
File "/Users/akrebs/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 493, in setWordInfo  
cmd_desc = resolve_cmd_desc(word_info, command_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/akrebs/Library/Application Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/clix/_types.py", line 85, in resolve_cmd_desc  
winfo.cmd_desc.proxy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
animations in bundle ChimeraX-Animations:  
trying to register unknown command: animations  
  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
animations in bundle ChimeraX-Animations:  
trying to register unknown command: animations  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,8
      Model Number: Z1FF000SDSM/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 23 days, 34 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P3223QE:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1050 x 1680
          UI Looks like: 1050 x 1680 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: 90


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    appdirs: 1.4.4
    appnope: 0.1.4
    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: 2025.7.14
    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: 1.61.5
    ChimeraX-AtomicLibrary: 14.2.2
    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-clix: 0.2.7
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202512132024
    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: 1.8
    ChimeraX-Label: 1.3
    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: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.5.4
    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: 1.7
    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: 1.50
    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
    contourpy: 1.3.3
    coverage: 7.13.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.18
    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
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    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
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    ipywidgets: 8.1.8
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    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
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    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
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
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    prompt_toolkit: 3.0.52
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    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
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    Pygments: 2.18.0
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    PyOpenGL-accelerate: 3.1.10
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    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
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    pytest-cov: 7.0.0
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    python-multipart: 0.0.20
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    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
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    rpds-py: 0.30.0
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
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    starlette: 0.50.0
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    traitlets: 5.14.3
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    typing_extensions: 4.15.0
    tzdata: 2025.3
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    uvicorn: 0.38.0
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    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0