Opened 6 months ago
Closed 6 months ago
#17554 closed defect (not a bug)
Test crash
| Reported by: | Eric Pettersen | Owned by: | Eric Pettersen |
|---|---|---|---|
| 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.