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#4959 closed defect (can't reproduce)
Crash opening mmCIF
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | 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-10-10.0.18362
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Thread 0x00001ad8 (most recent call first):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 306 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 558 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 1252 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 932 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 890 in _bootstrap
Thread 0x00001eb4 (most recent call first):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 306 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 558 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 1252 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 932 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 890 in _bootstrap
Current thread 0x00000c64 (most recent call first):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\mmcif\__init__.py", line 40 in open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 421 in collated_open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 179 in provider_open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 118 in cmd_open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\dialog.py", line 155 in _qt_safe
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 1015 in
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 194 in _run_module_as_main
Windows fatal exception: access violation
Thread 0x00001ad8 (most recent call first):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 306 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 558 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 1252 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 932 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 890 in _bootstrap
Thread 0x00001eb4 (most recent call first):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 306 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 558 in wait
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 1252 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 932 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py", line 890 in _bootstrap
Current thread 0x00000c64 (most recent call first):
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\mmcif\__init__.py", line 40 in open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 421 in collated_open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 179 in provider_open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\cmd.py", line 118 in cmd_open
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\open_command\dialog.py", line 155 in _qt_safe
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 1015 in
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 194 in _run_module_as_main
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 - Build 27.20.100.8984
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteOne 800 G4 23.8-in Non-Touch AiO
OS: Microsoft Windows 10 Enterprise (Build 18363)
Memory: 16,948,420,608
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
OSLanguage: en-US
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (5)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash opening mmCIF |
comment:2 by , 4 years ago
comment:3 by , 4 years ago
As of 2/17/2021 (so including 1.2.5 build) none of those are limited. The only limited attribute is IDATM type, which is not set by any input reader.
comment:4 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
need the mmCIF file that caused the problem to reproduce
Note:
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Do we currently have any string length limitations for atom names, residue names, chain names where buffer overflows could occur in reading and cause a crash?