Opened 6 months ago
Closed 6 months ago
#17554 closed defect (not a bug)
Test crash
Reported by: | pett | Owned by: | pett |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Platform | Version: | |
Keywords: | Cc: | Tom Goddard | |
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.dev202504290649 (2025-04-29 06:49:05 UTC) Description Last time you used ChimeraX it crashed. Used open dialog once and save dialog once. Fatal Python error: Aborted Thread 0x00000d38 (most recent call first): File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\selectors.py", line 314 in _select File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\selectors.py", line 323 in select File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\asyncio\base_events.py", line 1884 in _run_once File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\asyncio\base_events.py", line 607 in run_forever File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\tornado\platform\asyncio.py", line 205 in start File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\iostream.py", line 92 in _thread_main File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\threading.py", line 975 in run File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\threading.py", line 995 in _bootstrap Thread 0x00000410 (most recent call first): File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\threading.py", line 320 in wait File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\threading.py", line 622 in wait File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\history.py", line 903 in run File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\history.py", line 61 in only_when_enabled File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\decorator.py", line 235 in fun File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\threading.py", line 995 in _bootstrap Current thread 0x00000414 (most recent call first): File "C:\Users\pett\AppData\Local\Temp\ipykernel_6588\518143115.py", line 1 in File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\interactiveshell.py", line 3577 in run_code File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\interactiveshell.py", line 3517 in run_ast_nodes File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\interactiveshell.py", line 3334 in run_cell_async File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\async_helpers.py", line 128 in _pseudo_sync_runner File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\interactiveshell.py", line 3130 in _run_cell File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\IPython\core\interactiveshell.py", line 3075 in run_cell File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\zmqshell.py", line 549 in run_cell File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\ipkernel.py", line 449 in do_execute File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\kernelbase.py", line 778 in execute_request File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\ipkernel.py", line 362 in execute_request File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\inprocess\ipkernel.py", line 81 in execute_request File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\kernelbase.py", line 437 in dispatch_shell File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\asyncio\events.py", line 80 in _run File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\asyncio\base_events.py", line 1922 in _run_once File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\asyncio\base_events.py", line 607 in run_forever File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\asyncio\base_events.py", line 640 in run_until_complete File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\jupyter_core\utils\__init__.py", line 165 in wrapped File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\inprocess\client.py", line 195 in _dispatch_to_kernel File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\ipykernel\inprocess\client.py", line 119 in execute File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\frontend_widget.py", line 288 in _execute File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\console_widget.py", line 680 in do_execute File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\history_console_widget.py", line 42 in do_execute File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\console_widget.py", line 605 in _trigger_is_complete_callback File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\console_widget.py", line 600 in _handle_is_complete_reply File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\base_frontend_mixin.py", line 138 in _dispatch File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\inprocess.py", line 46 in call_handlers File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\qtconsole\inprocess.py", line 42 in File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init File "C:\Program Files\ChimeraX-Apr-29-2025\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: _win32sysloader, win32api, win32com.shell.shell, chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imaging, PIL._imagingmath, psutil._psutil_windows, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, zmq.backend.cython._zmq, tornado.speedups, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PyQt6.QtSvg, _pydevd_bundle.pydevd_cython (total: 59) ===== Log before crash start ===== UCSF ChimeraX version: 1.10.dev202504290649 (2025-04-29) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/pett/Downloads/ChimeraX/PDB/2src.cif 2src.cif title: Crystal structure of human tyrosine-protein kinase C-SRC, In complex with amp- PNP [more info...] Chain information for 2src.cif #1 --- Chain | Description | UniProt A | TYROSINE-PROTEIN KINASE SRC | SRC_HUMAN 83-533 Non-standard residues in 2src.cif #1 --- ANP — phosphoaminophosphonic acid-adenylate ester > save C:/Users/pett/test-save.cxs > ui tool show Shell 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. QWaitCondition: Destroyed while threads are still waiting ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.dev202504290649 (2025-04-29) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 NVIDIA 560.94 OpenGL renderer: NVIDIA GeForce RTX 4070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: windows Manufacturer: Gigabyte Technology Co., Ltd. Model: To be filled by O.E.M. OS: Microsoft Windows 10 Home (Build 19045) Memory: 66,135,482,368 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz OSLanguage: en-US 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: 3.3.1 build: 1.2.2.post1 certifi: 2025.4.26 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: 2.20.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.17 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 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: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.6 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202504290649 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: 1.6.1 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: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 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: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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: 2.7.9 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: 1.1.3 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: 1.45.1 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: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.57.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 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: 8.1.6 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.14 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 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: 2.1.3 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 plotly: 5.24.1 pluggy: 1.5.0 prompt_toolkit: 3.0.51 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 pyKVFinder: 0.7.1 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: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pywin32: 310 pyzmq: 26.4.0 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: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.7 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 tenacity: 9.0.0 tifffile: 2025.3.13 tinyarray: 1.2.4 toml: 0.10.2 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 WMI: 1.5.1
Change History (2)
comment:1 by , 6 months ago
Cc: | added |
---|---|
Component: | Unassigned → Platform |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Test crash |
comment:2 by , 6 months ago
Resolution: | → not a bug |
---|---|
Status: | accepted → closed |
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Crash via os.abort() having used open dialog once and save dialog once. Still looks good.