Crash in chem_group on Windows

[amaillard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202503260000 (2025-03-26 00:00:48 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
- 1st crash occured during electrostatic surfaces calculations in a session containing several cif files from alphafold3 (launched from toolbar; all models were shown)
- I've checked that calculations are OK for every cif file used in that session
- except for once, where chimera managed to calculate the electrostatic surface a single molecule (other models hidden), all my attempts have led to a crash, even when only two models had been loaded and only one was shown (yes, that's unlike the exception I have mentioned)
- please note, sometimes I have started fresh and sometimes I have opened the session that had crashed. Maybe this could explain the apparent contradiction above.

Windows fatal exception: Windows fatal exception: access violation

Thread 0x00003ee8Windows fatal exception: access violation

access violation

 (most recent call first):
  File "Windows fatal exception: access violation

Windows fatal exception: access violation

C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002460 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 771 in _find_acceptors
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\addh\hbond.py", line 259 in add_hydrogens
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\addh\cmd.py", line 184 in hbond_add_hydrogens
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\addh\cmd.py", line 77 in cmd_addh
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\coulombic\coulombic.py", line 95 in assign_charges
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\coulombic\cmd.py", line 102 in cmd_coulombic
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 537 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 594 in run_expanded_command
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 72 in func_plus_tip
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 340 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 421 in run_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 403 in try_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1394 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503260000\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 =====
> open "C:\Users\amaillard\Downloads\SOFT\Bio-structure\ChimeraX 1.10
> fixed\native_save.py"

executed native_save.py  
UCSF ChimeraX version: 1.10.dev202503260000 (2025-03-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\amaillard\Documents\Pseudo\MyPDB\250423 AF3 ExlA fringe &
> pore\pdb\ExlA_Arg variants.cxs" format session

> view name session-start

opened ChimeraX session  

> close #3-5

> hide #2 models

> coulombic #1


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

Log:
> open "C:\Users\amaillard\Downloads\SOFT\Bio-structure\ChimeraX 1.10
> fixed\native_save.py"

executed native_save.py  
UCSF ChimeraX version: 1.10.dev202503260000 (2025-03-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 377.83
OpenGL renderer: Quadro 600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: fr_FR.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7010
OS: Microsoft Windows 10 Entreprise (Build 19045)
Memory: 17,132,265,472
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
OSLanguage: fr-FR

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    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: 2.2.7
    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.dev202503260000
    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: 1.5.3
    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
    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: 2.16
    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: 1.1.1
    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: 2.17.1
    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: 1.4.10
    contourpy: 1.3.1
    coverage: 7.7.1
    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: 3.18.0
    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: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    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
    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: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    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: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.3.0
    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: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    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: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.0
    tzdata: 2025.2
    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

[pett]

Hi Antoine,

Thanks for reporting this problem. We implemented a fix about three weeks ago that solves at least some of these crashes. Could you try the current daily build and see if you still get crashes? If you do, a recipe for reproducing the crash would really help.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[antoine.maillard@…]

Hi Eric,

Bugs fixed! All electrostatic surfaces have been calculated smoothly.
Next time I meet a bug in a daily build, I'll test the latest one before reporting.
Once again, thank you very much!

Antoine


IBS - Bât92 p367
+33 4 57 42 86 08

----- Mail original -----
De: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
À: "Antoine Maillard" <amaillard@ibs.fr>, "Eric Pettersen" <pett@cgl.ucsf.edu>
Envoyé: Lundi 28 Avril 2025 20:23:42
Objet: Re: [ChimeraX] #17500: Crash in chem_group on Windows

#17500: Crash in chem_group on Windows
-----------------------------------------+----------------------
          Reporter:  amaillard@\u2026         |      Owner:  pett
              Type:  defect              |     Status:  feedback
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback

Comment:

 Hi Antoine,
         Thanks for reporting this problem.  We implemented a fix about
 three weeks ago that solves at least some of these crashes.  Could you try
 the current daily build and see if you still get crashes?  If you do, a
 recipe for reproducing the crash would really help.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

[pett]

I'm glad to hear that the latest version works for you.

--Eric