Opened 4 years ago

Closed 4 years ago

#5841 closed defect (duplicate)

Crash showing side view

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
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.
Windows fatal exception: access violation

Current thread 0x00003930 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 235 in swap_buffers
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 496 in swap_buffers
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 179 in draw
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\sideview\tool.py", line 276 in render
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\sideview\tool.py", line 116 in exposeEvent
  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 =====
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 https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> open 7kkj

Summary of feedback from opening 7kkj fetched from pdb  
---  
notes | Fetching compressed mmCIF 7kkj from
http://files.rcsb.org/download/7kkj.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
  
7kkj title:  
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]  
  
Chain information for 7kkj #1  
---  
Chain | Description  
A C | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkj #1  
---  
CL — chloride ion  
SO4 — sulfate ion  
  
7kkj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select /A:1-118

1762 atoms, 1781 bonds, 118 residues, 1 model selected  

> log metadata #1

> sym #1 assembly 1

> view

> close #2

> show #1 models

> show sel target ab

> hide sel cartoons

> style sel sphere

Changed 1762 atom styles  

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting full

> lighting soft

> select /C:63

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

61 atoms, 60 bonds, 4 residues, 1 model selected  

> select up

1841 atoms, 1792 bonds, 187 residues, 1 model selected  

> color sel bychain

> color sel byhetero

> rainbow sel

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> lighting full

> lighting soft

> lighting simple

> lighting full

> show sel surfaces

> select clear

> show surfaces

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/C SER 119 OG  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 7kkj_A SES surface #1.2: minimum, -14.35, mean 1.79,
maximum 15.82  
Coulombic values for 7kkj_C SES surface #1.1: minimum, -13.58, mean 1.82,
maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!1 models

> show #!1 models

> mlp

Map values for surface "7kkj_A SES surface": minimum -26.08, mean -5.439,
maximum 21.88  
Map values for surface "7kkj_C SES surface": minimum -26.27, mean -5.542,
maximum 20.74  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor

3683 atoms, 373 residues, 2 surfaces, atom bfactor range 18.9 to 93.5  

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> transparency 50

> volume style surface

No volumes specified  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> show surfaces

> coulombic

Coulombic values for 7kkj_A SES surface #1.2: minimum, -14.35, mean 1.79,
maximum 15.82  
Coulombic values for 7kkj_C SES surface #1.1: minimum, -13.58, mean 1.82,
maximum 16.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting soft

> lighting full

> lighting soft

> color byhetero

> color bychain

> rainbow

> color bypolymer

> color bychain

> lighting flat

> transparency 50

Alignment identifier is 1  

> select /A-C:68

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select /A-C:68-73

200 atoms, 200 bonds, 12 residues, 1 model selected  

> select /A-C:68

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select /A-C:68-73

200 atoms, 200 bonds, 12 residues, 1 model selected  

> color (#!1 & sel) red

> select clear

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> open 7kkj from ads

No such database 'ads'  

> open 7kkj fromDatabase eds

Summary of feedback from opening 7kkj fetched from eds  
---  
note | Fetching map 7kkj from
http://www.ebi.ac.uk/pdbe/coordinates/files/7kkj.ccp4  
  
Opened eds 7kkj as #2, grid size 118,103,128, pixel 0.619,0.594,0.611, shown
at level 1.16, step 1, values float32  

> hide cartoons

> show atoms

> volume #2 showOutlineBox true

> volume zone #2 nearAtoms #1 range 3.71

> hide H

> ui tool show "Side View"


===== 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  




OpenGL version: 3.3.0 NVIDIA 466.27
OpenGL renderer: NVIDIA GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GF65 Thin 9SEXR
OS: Microsoft Windows 11 Pro (Build 22000)
Memory: 17,013,776,384
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: pt-PT
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: 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 (2)

comment:1 by pett, 4 years ago

Cc: Greg Couch added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash showing side view

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Side View just shown, got an expose event, was drawn with OpenGL and then crashed on OpenGL swap buffers. Seems like a graphics driver crash, but maybe a Qt bug where the window was bit actually ready to draw even though the expose event was sent. Have seen this reported before. If it happens in Qt 6 can try putting in delay in drawing after expose.

Note: See TracTickets for help on using tickets.