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Opened 3 years ago
Closed 3 years ago
#7412 closed defect (can't reproduce)
Crash in set_matrix after sym command
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.18.0-3-amd64-x86_64-with-glibc2.33
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00007f63d60c3740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2776 in set_matrix
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 791 in set_model_matrix
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 817 in _draw_geometry
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 759 in draw_self
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 752 in draw
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1539 in _draw_multiple
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1526 in draw_opaque
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/view.py", line 235 in _draw_scene
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/view.py", line 165 in draw
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 2bbv
Summary of feedback from opening 2bbv fetched from pdb
---
notes | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description | UniProt
A B C | protein (black beetle virus capsid protein) | COAT_BBV
D E F | protein (black beetle virus capsid protein) | COAT_BBV
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> color bychain
> style /b stick
Changed 2382 atom styles
> color /n teal
> hide #1.2 models
> hide #1.1 models
> show #1.1 models
> show #1.2 models
> hide /c
> ribbon /c
> select /n:4@C5'
1 atom, 1 residue, 1 model selected
> hide
> ~ribbon
> show
> ~display
> display
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel gold
> select clear
> surface #1
> ~display
> color /n fromatoms
> color bychain
> color /n fromatoms
> style solvent shpere
Expected a keyword
> display
> style solvent sphere
Changed 208 atom styles
> color solvent red
> color /a fromatoms
> color /b fromatoms
> color fromatoms
> color fromatoms surfaces
> color fromatoms
> sym #1
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly| 60 copies of chains A-F,N
2| icosahedral asymmetric unit| 1 copy of chains A-F,N
3| icosahedral pentamer| 5 copies of chains A-F,N
4| icosahedral 23 hexamer| 6 copies of chains A-F,N
5| icosahedral asymmetric unit, std point frame| 1 copy of chains A-F,N
6| crystal asymmetric unit, crystal frame| 5 copies of chains A-F,N
> colose @
Unknown command: colose @
> colose #2
Unknown command: colose #2
> close #2
> show #1 models
> close
> open 2bbv
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description | UniProt
A B C | protein (black beetle virus capsid protein) | COAT_BBV
D E F | protein (black beetle virus capsid protein) | COAT_BBV
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> surface
> hide
> color /n fromatoms
> sym #1 assembly 3
> newmodel false
Unknown command: newmodel false
> close #2
> show #1 models
> sym #1 assembly 3 newmodels false copies false
Expected a keyword
> sym #1 assembly 3 newModel false copies false
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.2 (Core Profile) Mesa 22.2.0-rc1
OpenGL renderer: Mesa Intel(R) HD Graphics 4000 (IVB GT2)
OpenGL vendor: Intel
Python: 3.9.11
Locale: it_IT.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb
XDG_SESSION_TYPE=tty
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=:0
Manufacturer: LENOVO
Model: 232566G
OS: Debian GNU/Linux unstable sid
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i7-3520M CPU @ 2.90GHz
Cache Size: 4096 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 3.4Gi 920Mi 264Mi 10Gi 11Gi
Swap: 7.4Gi 0B 7.4Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation 3rd Gen Core processor Graphics Controller [8086:0166] (rev 09)
Subsystem: Lenovo 3rd Gen Core processor Graphics Controller [17aa:21fa]
Kernel driver in use: i915
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
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: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in set_matrix after sym command |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Maybe a graphics driver crash. Was setting a shader variable which should never cause a crash