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#5953 closed defect (can't reproduce)
Crash after H-bonds shown
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | 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-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00000c88 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000c74 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Current thread 0x0000299c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open "D:\作图\ABC CryC dock\A1.00.pdb" format pdb
Summary of feedback from opening D:\作图\ABC CryC dock\A1.00.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for A1.00.pdb
---
Chain | Description
1.1/A | No description available
1.2/A 1.2/B | No description available
> select #1.1
8096 atoms, 8258 bonds, 843 residues, 1 model selected
> hide #1.2 models
> preset sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> ~select #1.1
Nothing selected
> select #1.1
8096 atoms, 8258 bonds, 843 residues, 1 model selected
> ~select #1.1
Nothing selected
> select #1.1
8096 atoms, 8258 bonds, 843 residues, 1 model selected
> style sel ball
Changed 8096 atom styles
> select #1.2
22698 atoms, 23134 bonds, 2316 residues, 1 model selected
> ~select #1.2
Nothing selected
> color #1.1 #04d264 transparency 0
> hbonds reveal true
3752 hydrogen bonds found
> hbonds reveal true
3752 hydrogen bonds found
> lighting simple
> ui tool show "Side View"
> lighting full
> lighting soft
> ui tool show "Side View"
> view
> view orient
> view
> ui tool show "Side View"
> set bgColor white
> set bgColor black
> ui tool show "Side View"
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> show cartoons
> show atoms
> hide #!1.1 models
> hide #!1.2 cartoons
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> show atoms
> hide atoms
> show atoms
> hide atoms
> show cartoons
> show atoms
> show cartoons
> show atoms
> hide atoms
> hide #!1.1 models
> show #!1.2 atoms
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 cartoons
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 atoms
> show #!1.2 cartoons
> show #!1.1 models
> hbonds reveal true
3752 hydrogen bonds found
> hide #!1.1 models
> hide #!1.2 cartoons
> hide #!1.2 atoms
> hide #!1.2 cartoons
> show #!1.2 cartoons
> show #!1.2 atoms
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 cartoons
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> show cartoons
> hide atoms
> hide #!1.2 models
> show #!1.1 atoms
> hide #!1.1 atoms
> show #!1.2 models
> hide #!1.1 models
> show #!1.2 atoms
> show #!1.1 models
> hide atoms
> show atoms
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> hide #!1.1 atoms
> show #!1.2 models
> hide #!1.1 models
> hide #!1.2 cartoons
> show #!1.2 cartoons
> hide #!1.2 cartoons
> show #!1.2 cartoons
> hide #!1.2 cartoons
> hide #!1.2 atoms
> show #!1.2 atoms
> show #!1.2 cartoons
> hide #!1.2 cartoons
> show #!1.2 cartoons
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hbind:sti reveal true log true
Unknown command: hbind:sti reveal true log true
> hbond:sti reveal true log true
Unknown command: hbond:sti reveal true log true
> hbonds:sti reveal true log true
Unknown command: hbonds:sti reveal true log true
> ui tool show H-Bonds
> hbonds reveal true
3752 hydrogen bonds found
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\作图\ABC CryC dock\A1.00.pdb" format pdb
Summary of feedback from opening D:\作图\ABC CryC dock\A1.00.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for A1.00.pdb
---
Chain | Description
1.1/A | No description available
1.2/A 1.2/B | No description available
OpenGL version: 3.3.0 NVIDIA 445.75
OpenGL renderer: GeForce GT 710/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Suma
Model: W3335HA1
OS: Microsoft Windows 10 专业版 (Build 19043)
Memory: 8,483,012,608
MaxProcessMemory: 137,438,953,344
CPU: 16 Hygon C86 3250 8-core Processor
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
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: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
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: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (3)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Analysis |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash after H-bonds shown |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 4 years ago
hbonds completed since it reported how many it found. And the crash was as usual in the event loop.
Again this use seems to have a Chinese language locale, and the error says "Fatal Python error: Aborted", rather than the more common Windows fatal error of "access violation". I suspect this "Aborted" means Qt knew what it was doing and called abort() and probably emitted a fatal error message before doing so. If we had that error message we would probably understand what is going on. I made a ticket for getting those Qt fatal error messages into the bug report. A simple scheme is to just write them into the current file that is receiving the python faulthandler messages.
Note:
See TracTickets
for help on using tickets.
Wasn't the first time the hbonds command was used in the session.