Opened 6 months ago
Closed 6 months ago
#17337 closed defect (duplicate)
Crash in chem_group on Windows
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Analysis | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.10.dev202504020144 (2025-04-02 01:44:35 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 Thread 0x0000160cWindows fatal exception: access violation (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 324 in wait File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 622 in wait File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1392 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00001fdc (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00003060 (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00003264 (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\connection.py", line 878 in wait File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00002788 (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x000009d8 (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x000023dc (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00001078 (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00000fe0 (most recent call first): File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 771 in _find_acceptors File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\addh\hbond.py", line 259 in add_hydrogens File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\addh\cmd.py", line 184 in hbond_add_hydrogens File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\addh\cmd.py", line 77 in cmd_addh File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\coulombic\coulombic.py", line 95 in assign_charges File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\coulombic\cmd.py", line 102 in cmd_coulombic File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 537 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 594 in run_expanded_command File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 72 in func_plus_tip File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 340 in run File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 421 in run_shortcut File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 403 in try_shortcut File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1394 in run_provider File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init File "D:\Program Files\ChimeraX 1.10.dev202504020144\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 ===== > ui mousemode right clip > ui mousemode right "clip rotate" > ui mousemode right clip > show cartoons > show surfaces > show target m > color byelement > color byhetero > color byelement > color black > color lime > mlp Map values for surface "AF-A6ZIB7-F1-model_v4.pdb_A SES surface": minimum -29.54, mean -2.111, maximum 24.99 To also show corresponding color key, enter the above mlp command and add key true > coulombic ===== Log before crash end ===== Log: Startup Messages --- warning | Your computer has Intel graphics driver 8190 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this. UCSF ChimeraX version: 1.10.dev202504020144 (2025-04-02) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\\\Users\\\ZHANG\\\Desktop\\\3dd5.pdb 3dd5.pdb title: Glomerella cingulata E600-cutinase complex [more info...] Chain information for 3dd5.pdb #1 --- Chain | Description | UniProt A B C D E F G H | cutin hydrolase | CUTI_COLGL 31-224 Non-standard residues in 3dd5.pdb #1 --- DEP — diethyl phosphonate OpenGL version: 3.3.0 - Build 27.20.100.8190 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel 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: 90J4000FCD OS: Microsoft Windows 10 家庭中文版 (Build 19045) Memory: 8,468,692,992 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i3-8100 CPU @ 3.60GHz OSLanguage: zh-CN 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: 3.2.1 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: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20 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.dev202504020144 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: 2.8 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: 1.45 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: 7.8.0 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: 3.10.1 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: 6.1.0 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
Change History (2)
comment:1 by , 6 months ago
Component: | Unassigned → Structure Analysis |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Crash in chem_group on Windows |
comment:2 by , 6 months ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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