pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)

[ubaumann@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Tools--> Analysis --> find cavities

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3qm7

Summary of feedback from opening 3qm7 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3qm7 from http://files.rcsb.org/download/3qm7.cif  
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif  
  
3qm7 title:  
Blackfin tuna carbonmonoxy-myoglobin, atomic resolution [more info...]  
  
Chain information for 3qm7 #1  
---  
Chain | Description  
A | Myoglobin  
  
Non-standard residues in 3qm7 #1  
---  
ACE — acetyl group  
CMO — carbon monoxide  
EDO — 1,2-ethanediol (ethylene glycol)  
HEM — protoporphyrin IX containing Fe (HEME)  
  
310 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select :HOH

152 atoms, 152 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

[Repeated 1 time(s)]

> select clear

> select :HOH &SAS=0

Expected a keyword  

> select :HOH & SAS=0

Expected a keyword  

> ui tool show "Render/Select by Attribute"

> ui tool show "Check Waters"

> hbonds /A:301-452 interModel false reveal true restrict any name "water
> H-bonds"

342 hydrogen bonds found  

> select /A:301-452

152 atoms, 184 pseudobonds, 152 residues, 2 models selected  

> display /A:301-452 :<4

> view /A:301-452 @<4

> 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.  
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.5
which is incompatible.  
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.2.5 which is incompatible.  
\---  

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

> kvfinder

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities  
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,  
File
"/Applications/ChimeraX-1.9.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
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder  
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
ImportError: dlopen(/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
ImportError: dlopen(/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
File "/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
  
See log for complete Python traceback.  
  

> select clear

> ui tool show "Find Cavities"

> kvfinder

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities  
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,  
File
"/Applications/ChimeraX-1.9.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
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder  
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
ImportError: dlopen(/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
ImportError: dlopen(/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/ubaumann/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
File "/Users/ubaumann/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3D/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 1 day, 19 hours, 6 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        ASUS CG32U:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 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


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    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: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    narwhals: 1.35.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.2.5
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 6.0.1
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.3
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[pett]

Hi Ulrich,

Thanks for reporting this problem. The issue is with the underlying pyKVFinder module that ChimeraX downloads from PyPi to carry out the cavity detection. There is an issue open on their GitHub page about this problem (​https://github.com/LBC-LNBio/pyKVFinder/issues/160). I will add you to the recipient list for the ticket we have open in the ChimeraX bug-tracking database for this, so that you will be notified when it is resolved.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab