Crash in chem_group on Windows

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202501242328 (2025-01-24 23:28:17 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x000078b4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\ssl.py", line 1346 in do_handshake
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\ssl.py", line 1075 in _create
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\ssl.py", line 517 in wrap_socket
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\http\client.py", line 1458 in connect
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\http\client.py", line 979 in send
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\http\client.py", line 1041 in _send_output
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\http\client.py", line 1281 in endheaders
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\http\client.py", line 1332 in _send_request
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\http\client.py", line 1286 in request
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\urllib\request.py", line 1348 in do_open
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\urllib\request.py", line 1391 in https_open
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\urllib\request.py", line 496 in _call_chain
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\urllib\request.py", line 536 in _open
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\urllib\request.py", line 519 in open
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\urllib\request.py", line 216 in urlopen
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 516 in reload_available
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x00005138 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: access violation

Thread 0x00005138 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 770 in _find_acceptors
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\hbonds\cmd.py", line 94 in cmd_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3213 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\hbonds\tool.py", line 53 in run_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
  File "C:\Program Files\ChimeraX 1.10.dev202501242328\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501242328 (2025-01-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

getting structure  

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

getting structure  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 2 residues, 2 models selected  

> select down

15 atoms, 16 bonds, 1 residue, 1 model selected  

> ui mousemode right select

Drag select of 1 bonds  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 16 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,-2.9505,0,1,0,0.41238,0,0,1,-0.068415

> view matrix models #1,1,0,0,-2.6376,0,1,0,0.43116,0,0,1,-0.065104

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

16 atoms, 17 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,3.8498,0,1,0,2.5599,0,0,1,-0.092353

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.40192,0.91492,0.037102,4.0651,0.89908,-0.38664,-0.20532,2.2321,-0.17351,0.11588,-0.97799,-0.083871

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 16 bonds, 1 residue, 1 model selected  

> view matrix models
> #1,0.99341,0.041283,0.1069,-2.64,-0.060118,0.98192,0.17948,0.41387,-0.097555,-0.18472,0.97794,-0.091498

> view matrix models
> #1,0.99772,0.02066,-0.064261,-2.6385,-0.012505,0.9921,0.12481,0.4276,0.066332,-0.12372,0.9901,-0.044534

> view matrix models
> #1,0.9996,0.028426,-0.00052262,-2.638,-0.02812,0.99123,0.12915,0.42307,0.0041894,-0.12909,0.99162,-0.062529

> ui mousemode right select

> select clear

Drag select of 1 atoms  

> select up

15 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

31 atoms, 33 bonds, 2 residues, 2 models selected  

> select down

15 atoms, 16 bonds, 1 residue, 1 model selected  
Drag select of 1 atoms  

> select up

15 atoms, 16 bonds, 1 residue, 1 model selected  

> select clear

> select #1/a:1@C5

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 16 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.9996,0.028426,-0.00052262,-1.7945,-0.02812,0.99123,0.12915,0.54025,0.0041894,-0.12909,0.99162,-0.10755

> select clear

> ui tool show H-Bonds

> hbonds reveal true


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501242328 (2025-01-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 556.12
OpenGL renderer: NVIDIA GeForce GTX 1650 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 7501
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 16,929,980,416
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.12.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.18
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60
    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: 1.0.2
    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: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202501242328
    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: 1.2.7
    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: 1.5.1
    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: 2.7.7
    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-ProfileGrids: 1.0.1
    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: 2.15
    ChimeraX-Shape: 1.1
    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: 1.19.1
    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: 2.5.1
    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: 1.43
    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
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.10
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.12
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.15.4
    fonttools: 4.55.6
    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
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    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: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    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
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.18
    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: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1