Opened 10 months ago

Closed 7 months ago

Last modified 7 months ago

#16523 closed defect (fixed)

Crash in chem_group on Windows

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc: chimera-programmers, julio.bonilla@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-11-10.0.26100-SP0
ChimeraX Version: 1.10.dev202412222331 (2024-12-22 23:31:10 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: Windows fatal exception: access violationaccess violationWindows fatal exception: 

access violation

Thread 0x

Windows fatal exception: access violation0000285c (most recent call first):


Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 770 in _find_acceptors
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\hbonds\cmd.py", line 94 in cmd_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3213 in run
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 536 in run
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 593 in run_expanded_command
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 339 in run
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 420 in run_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 402 in try_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1386 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202412222331\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 =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202412222331 (2024-12-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> open C:/Users/aqmm7/Downloads/1ca4.pdb

1ca4.pdb title:  
Structure of TNF receptor associated factor 2 (TRAF2) [more info...]  
  
Chain information for 1ca4.pdb #1  
---  
Chain | Description | UniProt  
A B C D E F | TRAF2 | TRAF2_HUMAN 334-501  
  

> hide cartoons

> show cartoons

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
~~~~~~~~~~^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1906, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 363, in update_graphics_if_needed  
self._create_ribbon_graphics()  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 673, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\atomic\ribbon.py", line 630, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\atomic\ribbon.py", line 180, in _make_ribbon_graphics  
_ribbon_geometry(path, display_ranges, len(residues), xs_front, xs_back,
geometry,  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
radial_scale=radial_scale)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\atomic\ribbon.py", line 477, in _ribbon_geometry  
_ribbons.ribbon_extrusions(centers, tangents, normals, ranges,  
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
num_res, xsf, xsb, geometry._geom_cpp, **radial_scale_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: Array argument has non-numeric values  
  
Error processing trigger "graphics update":  
TypeError: Array argument has non-numeric values  
  
File "C:\Program Files\ChimeraX 1.10.dev202412222331\bin\Lib\site-
packages\chimerax\atomic\ribbon.py", line 477, in _ribbon_geometry  
_ribbons.ribbon_extrusions(centers, tangents, normals, ranges,  
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
num_res, xsf, xsb, geometry._geom_cpp, **radial_scale_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> style stick

Changed 8435 atom styles  

> style ball

Changed 8435 atom styles  

> hide cartoons

> rainbow

> show target m

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> ui dockable false Toolbar

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> rainbow

> color byhetero

> color bychain

> hide #* target a

> show target ab

> select clear

> hide cartoons

> show cartoons

> show atoms

> open C:\Users\aqmm7\Downloads\1ca4.pdb format pdb

1ca4.pdb title:  
Structure of TNF receptor associated factor 2 (TRAF2) [more info...]  
  
Chain information for 1ca4.pdb #2  
---  
Chain | Description | UniProt  
A B C D E F | TRAF2 | TRAF2_HUMAN 334-501  
  

> view clip false

> log metadata #1

> log chains #1

Chain information for 1ca4.pdb #1  
---  
Chain | Description | UniProt  
A B C D E F | TRAF2 | TRAF2_HUMAN 334-501  
  

> log metadata #2

> log chains #2

Chain information for 1ca4.pdb #2  
---  
Chain | Description | UniProt  
A B C D E F | TRAF2 | TRAF2_HUMAN 334-501  
  

> hide atoms

> show atoms

> select add #1

8435 atoms, 7872 bonds, 1751 residues, 1 model selected  

> select add #2

16870 atoms, 15744 bonds, 3502 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\aqmm7/Desktop\movie1.mp4

Movie saved to C:\Users\aqmm7/Desktop\movie1.mp4  
  

> style sphere

Changed 16870 atom styles  

> show cartoons

> hbonds reveal true


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202412222331 (2024-12-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 Core Profile Context 23.19.14.08.240820
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.13.1
Locale: en_GB.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: HP
Model: HP Laptop 15s-eq2xxx
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 16,456,007,680
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5500U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    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: 2024.12.14
    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: 2.16.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.59
    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.dev202412222331
    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
    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: 3.5.7
    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: 1.42.2
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.9
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.11
    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: 2024.9.22
    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: 3.1.4
    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: 5.3.0
    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: 1.7.2
    networkx: 3.3
    nibabel: 5.2.0
    numexpr: 2.10.2
    numpy: 2.2.0
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.48
    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: 3.3.4
    pynrrd: 1.1.1
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine: 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: 308
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.1
    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.dev0
    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: 2024.2
    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

Change History (7)

comment:1 by Eric Pettersen, 10 months ago

Cc: chimera-programmers added
Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in chem_group on Windows

Can't get it to crash on my Mac, though the PDB version of 1ca4 could have differences from what the user used. Will try on Windows when I'm in the office.

comment:2 by Eric Pettersen, 7 months ago

Have not been able to reproduce on the Windows machines at work, even when the bug report was using completely standard PDB entries (there have been a total of 30 reports to date). All the reports are on 1.10, none on earlier versions.

comment:3 by Eric Pettersen, 7 months ago

Cc: julio.bonilla@… added

comment:4 by Zach Pearson, 7 months ago

This user's Python is reported as 3.13, and their build is from before Christmas. This is an old daily build from when we tried to upgrade Python. The user needs a new daily build.

comment:5 by Zach Pearson, 7 months ago

If they'd like to continue using Python 3.13, there is a techpreview out now.

comment:7 by Eric Pettersen, 7 months ago

Resolution: → fixed
Status: accepted → closed

With the help of #17278, I can see the crash is Ring::aromatic() called from find_aro_amines(). Other parts of the code had bulletproofing against the Ring disappearing from the .aromatic() call (due to IDATM types getting computed), but this (and one other call) didn't. I have added the bulletproofing which hopefully will fix this.

Fix: ​https://github.com/RBVI/ChimeraX/commit/1d859fc5f1a2e04c1fa8b03dd8dccf45acc6b2d9

Version 0, edited 7 months ago by Eric Pettersen (next)
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