ChimeraX bug report submission

[Mitch Murphy]

The following bug report has been submitted:
Platform:        macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.12.dev202601080343 (2026-01-08 03:43:52 UTC)
Description
PDB 5TAL, find cavities

Log:
UCSF ChimeraX version: 1.12.dev202601080343 (2026-01-08)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mitch/github/hmx/aspirin/5f1a-aspirin.psf coords
> /Users/mitch/github/hmx/aspirin/5f1a-aspirin.dump

Summary of feedback from opening
/Users/mitch/github/hmx/aspirin/5f1a-aspirin.psf  
---  
notes | * LAMMPS psf file via write_psf, version 10 Dec 2025, timestep = 0, units = real  
* II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I)  
* expanded format EXT:  
* (I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8) XPLOR  
* [https://userguide.mdanalysis.org/stable/formats/reference/psf.html]  
*** read_dump() (Safe Hybrid) 1.410412 seconds  
  
Chain information for 5f1a-aspirin.psf #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> distance :asa@h8 :530@hg1

Distance between /? ASA 100293 H8 and /A SER 530 HG1: 33.434Å  

> distance :asa@h8 :530@hg1

Distance already exists; modify distance properties with 'distance style'  

> show :530 atoms

> distance :asa@h8 :120@cz

Distance between /? ASA 100293 H8 and /A ARG 120 CZ: 22.530Å  

> show :120 atoms

> surface #1 transparency 50

> surface #1 transparency 20

> select :120,355,524

60 atoms, 58 bonds, 3 residues, 1 model selected  

> color sel byhetero

> select ~sel

170254 atoms, 119539 bonds, 1 pseudobond, 52107 residues, 3 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel surfaces

> select ~sel & ##selected

60 atoms, 64 bonds, 1 pseudobond, 3 residues, 2 models selected  

> hide sel surfaces

> close #1

> open /Users/mitch/github/hmx/aspirin/5f1a-aspirin.psf coords
> /Users/mitch/github/hmx/aspirin/5f1a-aspirin.dump

Summary of feedback from opening
/Users/mitch/github/hmx/aspirin/5f1a-aspirin.psf  
---  
notes | * LAMMPS psf file via write_psf, version 10 Dec 2025, timestep = 0, units = real  
* II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I)  
* expanded format EXT:  
* (I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8) XPLOR  
* [https://userguide.mdanalysis.org/stable/formats/reference/psf.html]  
*** read_dump() (Safe Hybrid) 1.374562 seconds  
  
Chain information for 5f1a-aspirin.psf #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> surface #1 transparency 20

> close #1

> open /Users/mitch/github/hmx/aspirin/5f1a-aspirin.psf coords
> /Users/mitch/github/hmx/aspirin/5f1a-aspirin.dump

Summary of feedback from opening
/Users/mitch/github/hmx/aspirin/5f1a-aspirin.psf  
---  
notes | * LAMMPS psf file via write_psf, version 10 Dec 2025, timestep = 0, units = real  
* II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I)  
* expanded format EXT:  
* (I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8) XPLOR  
* [https://userguide.mdanalysis.org/stable/formats/reference/psf.html]  
*** read_dump() (Safe Hybrid) 1.350861 seconds  
  
Chain information for 5f1a-aspirin.psf #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> surface #1 transparency 20

> hide :tip3

> select :530

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

> view sel

> show sel atoms

> select add #1

170284 atoms, 119583 bonds, 52100 residues, 6 models selected  

> hide sel surfaces

> open /Users/mitch/Downloads/tarball/step5_assembly.pdb

Summary of feedback from opening
/Users/mitch/Downloads/tarball/step5_assembly.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.1 ON JAN, 19.
2021. JOB  
  
Ignored bad PDB record found on line 2  
REMARK INPUT GENERATION  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 1/19/21 21: 3:41 CREATED BY USER: apache  
  

> close #1

> close #2

> select add #3

62905 atoms, 50605 bonds, 12173 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> show sel cartoons

> hide sel cartoons

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> view sel

> select add #3

62905 atoms, 50605 bonds, 12173 residues, 4 models selected  

> select subtract #3

1 model selected  

> hide :tip3

> hide #!3 models

> open 5TAL fromDatabase pdb format mmcif

Summary of feedback from opening 5TAL fetched from pdb  
---  
notes | Fetching compressed mmCIF 5tal from http://files.rcsb.org/download/5tal.cif  
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
Fetching CCD CFF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/CFF/CFF.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
5tal title:  
Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 1&2) [more info...]  
  
Chain information for 5tal #1  
---  
Chain | Description | UniProt  
A F H J | Peptidyl-prolyl cis-trans isomerase FKBP1B | FKB1B_HUMAN 0-107  
B E G I | Ryanodine receptor 1 | RYR1_RABIT 12-1275 1573-2479 2734-2939 3639-4253 4541-5037  
  
Non-standard residues in 5tal #1  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
CFF — caffeine (3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione)  
ZN — zinc ion  
  
76 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> select add #1

121456 atoms, 123776 bonds, 84 pseudobonds, 17220 residues, 3 models selected  

> view sel

> select :CFF

56 atoms, 60 bonds, 4 residues, 1 model selected  

> select :ZN

4 atoms, 4 residues, 1 model selected  

> select add #1

121456 atoms, 123776 bonds, 84 pseudobonds, 17220 residues, 3 models selected  

> transparency 20

> transparency #1 20

> transparency #1 80

> transparency #1 80 target a

> select subtract #1

Nothing selected  

> transparency #1 90 target a

> select :CA

4 atoms, 4 residues, 1 model selected  

> ui tool show Toolbar

> close #3

> select add #1

121456 atoms, 123776 bonds, 84 pseudobonds, 17220 residues, 3 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  

There are UNK residues in the structure. Charges in those regions will be
inaccurate.  

Coulombic values for 5tal_A SES surface #1.3: minimum, -13.76, mean -0.91,
maximum 13.21  
Coulombic values for 5tal_B SES surface #1.4: minimum, -32.48, mean -2.44,
maximum 14.75  
Coulombic values for 5tal_E SES surface #1.5: minimum, -32.57, mean -2.44,
maximum 14.26  
Coulombic values for 5tal_F SES surface #1.6: minimum, -13.93, mean -0.96,
maximum 13.25  
Coulombic values for 5tal_G SES surface #1.7: minimum, -30.64, mean -2.44,
maximum 15.72  
Coulombic values for 5tal_H SES surface #1.8: minimum, -13.89, mean -0.94,
maximum 13.34  
Coulombic values for 5tal_I SES surface #1.9: minimum, -40.88, mean -2.44,
maximum 13.77  
Coulombic values for 5tal_J SES surface #1.10: minimum, -13.66, mean -0.93,
maximum 13.55  
To also show corresponding color key, enter the above coulombic command and
add key true  

> ui tool show Animations

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  

Errors may have occurred when running pip:  

pip standard error:  
\---  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.4.1 which is incompatible.  
scipy 1.14.0 requires numpy<2.3,>=1.23.5, but you have numpy 2.4.1 which is
incompatible.  
\---  

pip standard output:  
\---  
\---  

pyKVFinder module installed from PyPi repository.  

> kvfinder

1198 cavities found for 5tal #1  
Traceback (most recent call last):  
File
"/Users/mitch/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 172, in find_cavities  
run(self.session, cmd)  
File
"/Users/mitch/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/mitch/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/mitch/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 141, in cmd_kvfinder  
contacting[cav_s] = contacting[k_index]  
~~~~~~~~~~^^^^^^^^^  
KeyError: 'KAA'  
  
KeyError: 'KAA'  
  
File
"/Users/mitch/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 141, in cmd_kvfinder  
contacting[cav_s] = contacting[k_index]  
~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
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: Mac16,7
      Model Number: FX2X3LL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 13822.61.10

Software:

    System Software Overview:

      System Version: macOS 26.2 (25C56)
      Kernel Version: Darwin 25.2.0
      Time since boot: 7 days, 17 hours, 12 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 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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
    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: 14.2.3
    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: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202601080343
    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-LightingGUI: 1.0
    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: 1.3.3
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    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: 1.7
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.2
    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: 7.13.1
    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: 7.1.0
    ipython: 9.9.0
    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: 8.7.0
    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
    narwhals: 2.15.0
    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: 2.4.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    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
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    plotly: 6.5.2
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    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: 0.8.4
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.1
    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
    pytz: 2025.2
    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: 2.8.1
    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: 3.1.2
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.13.3
    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: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0