Crash in chem_group on Windows

[zilongli822@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202503150710 (2025-03-15 07:10:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violationWindows fatal exception: access violationThread 0x0000a484 (most recent call first):




  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\threading.py", line 324 in wait
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\threading.py", line 622 in wait
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\threading.py", line 1392 in run
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000b1bc (most recent call first):
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 770 in _find_acceptors
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\addh\hbond.py", line 259 in add_hydrogens
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\addh\cmd.py", line 184 in hbond_add_hydrogens
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\addh\cmd.py", line 77 in cmd_addh
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\coulombic\coulombic.py", line 95 in assign_charges
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\coulombic\cmd.py", line 102 in cmd_coulombic
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 537 in run
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 594 in run_expanded_command
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 72 in func_plus_tip
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 340 in run
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 421 in run_shortcut
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 403 in try_shortcut
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1394 in run_provider
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "D:\ChimeraX\ChimeraX 1.10.dev202503150710\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
> coulombic


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

Log:
UCSF ChimeraX version: 1.10.dev202503150710 (2025-03-15)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 566.24
OpenGL renderer: NVIDIA GeForce RTX 4060 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: LENOVO
Model: 21LD
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 33,945,935,872
MaxProcessMemory: 137,438,953,344
CPU: 22 Intel(R) Core(TM) Ultra 9 185H
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.0
    build: 1.2.2.post1
    certifi: 2025.1.31
    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: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    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.dev202503150710
    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
    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: 2.1.7
    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: 2.15
    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: 1.14.1
    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: 1.0.2
    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
    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: 2.5.2
    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: 1.44
    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: 7.6.12
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.17.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    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: 3.1.6
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    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: 1.26.4
    OpenMM: 8.2.0
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    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: 4.3.6
    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: 0.32
    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: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
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    pytest: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 306
    pyzmq: 26.3.0
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    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: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
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    soupsieve: 2.6
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    sphinx-autodoc-typehints: 3.1.0
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    sphinxcontrib-devhelp: 2.0.0
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    stack-data: 0.6.3
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    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: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

[Eric Pettersen]

Hi Zilong,

Thanks for reporting this problem. Does it happen every time you add hydrogens? Only for particular structures? Every time for those structures? If so, is there any chance you could share one the structures where it happens (or it's PDB code if it's a standard PDB file)?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab