UnicodeDecodeError reading PDB file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\app\AUTODOCK\COA_4R4U.pdb format pdb

Summary of feedback from opening C:\app\AUTODOCK\COA_4R4U.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 5 ASP D 13 1 9  
Start residue of secondary structure not found: HELIX 2 2 PHE D 35 THR D 50 1
16  
Start residue of secondary structure not found: HELIX 3 3 PRO D 126 LEU D 130
1 5  
Start residue of secondary structure not found: HELIX 4 4 SER D 132 GLN D 139
1 8  
Start residue of secondary structure not found: HELIX 5 5 ASP D 191 SER D 203
1 13  
33 messages similar to the above omitted  
Cannot find LINK/SSBOND residue NA (302 )  
Cannot find LINK/SSBOND residue VAL (78 )  
Cannot find LINK/SSBOND residue NA (302 )  
Cannot find LINK/SSBOND residue NA (302 )  
Cannot find LINK/SSBOND residue NA (302 )  
1 messages similar to the above omitted  
  
COA_4R4U.pdb title:  
Crystal structure of acyl-coa thioesterase tesb from yersinia pestis In
complex with coenzyme A [more info...]  
  
Non-standard residues in COA_4R4U.pdb #1  
---  
COA — coenzyme A  
  

> open C:/postdoc/TE/TE4_4R4UCOA.pdb

Summary of feedback from opening C:/postdoc/TE/TE4_4R4UCOA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 3 LEU A 7 1 5  
Start residue of secondary structure not found: HELIX 2 2 GLY A 32 ALA A 42 1
11  
Start residue of secondary structure not found: HELIX 3 3 ALA A 43 THR A 46 1
4  
Start residue of secondary structure not found: HELIX 4 4 PRO A 122 ALA A 124
1 3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 139 GLU A 141
1 3  
41 messages similar to the above omitted  
  
Chain information for TE4_4R4UCOA.pdb  
---  
Chain | Description  
2.1/A 2.1/B | No description available  
  

> hide #1 models

> close #1

> close #2

> open C:\postdoc\TE\TE4_4R4UCOA.pdb format pdb

Summary of feedback from opening C:\postdoc\TE\TE4_4R4UCOA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 3 LEU A 7 1 5  
Start residue of secondary structure not found: HELIX 2 2 GLY A 32 ALA A 42 1
11  
Start residue of secondary structure not found: HELIX 3 3 ALA A 43 THR A 46 1
4  
Start residue of secondary structure not found: HELIX 4 4 PRO A 122 ALA A 124
1 3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 139 GLU A 141
1 3  
41 messages similar to the above omitted  
  
Chain information for TE4_4R4UCOA.pdb  
---  
Chain | Description  
1.1/A 1.1/B | No description available  
  

> open C:\postdoc\TE\TE4_4R4UCOA.pdb format pdb

Summary of feedback from opening C:\postdoc\TE\TE4_4R4UCOA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 3 LEU A 7 1 5  
Start residue of secondary structure not found: HELIX 2 2 GLY A 32 ALA A 42 1
11  
Start residue of secondary structure not found: HELIX 3 3 ALA A 43 THR A 46 1
4  
Start residue of secondary structure not found: HELIX 4 4 PRO A 122 ALA A 124
1 3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 139 GLU A 141
1 3  
41 messages similar to the above omitted  
  
Chain information for TE4_4R4UCOA.pdb  
---  
Chain | Description  
2.1/A 2.1/B | No description available  
  

> open C:\postdoc\TE\TE9.pdb format pdb

Chain information for TE9.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #!2 models

> hide #!1 models

> open C:\postdoc\TE\TE9_data_0915\Refine_15\TEs_refine_15.cif format mmcif

Summary of feedback from opening
C:\postdoc\TE\TE9_data_0915\Refine_15\TEs_refine_15.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 161  
Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for TEs_refine_15.cif #4  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> hide #4 models

> hide #3 models

> hide #2.2 models

> hide #!2.1 models

> hide #!1.1 models

> hide #1.2 models

> show #3 models

> show #4 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!1.1 models

> show #1.2 models

> show #!2 models

> show #!2.1 models

> show #2.2 models

> close #3

> close

> open C:\postdoc\TE\TE9_data_0915\Refine_7\TEs_refine_7.pdb format pdb

Traceback (most recent call last):  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 349, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\app\ChimeraX 1.10\bin\Lib\site-packages\chimerax\ui\gui.py", line
479, in thread_safe  
func(*args, **kw)  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 442, in defer  
cxcmd(session, topic)  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-packages\chimerax\pdb\\__init__.py",
line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-packages\chimerax\pdb\pdb.py", line
89, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd6 in position 37:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd6 in position 37:
invalid continuation byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  

> open C:/postdoc/TE/TE9_data_0915/Refine_7/TEs_refine_7.pdb

Traceback (most recent call last):  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 339, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-packages\chimerax\pdb\\__init__.py",
line 45, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\app\ChimeraX 1.10\bin\Lib\site-packages\chimerax\pdb\pdb.py", line
89, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen codecs>", line 322, in decode  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd6 in position 37:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd6 in position 37:
invalid continuation byte  
  
File "", line 322, in decode  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 572.97
OpenGL renderer: NVIDIA GeForce RTX 5060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Zephyrus G14 GA403WM_GA403WM
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 33,412,722,688
MaxProcessMemory: 137,438,953,344
CPU: 24 AMD Ryzen AI 9 HX 370 w/ Radeon 890M           
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2025.6.15
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-cuda-cupti-cu12: 12.9.79
    nvidia-cuda-nvcc-cu12: 12.9.86
    nvidia-cuda-nvrtc-cu12: 12.9.86
    nvidia-cuda-runtime-cu12: 12.9.79
    nvidia-cufft-cu12: 11.4.1.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Eric Pettersen]

Need the file