Opened 3 years ago

Closed 3 years ago

#6963 closed defect (can't reproduce)

Crash computing surface

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4.dev202201260121 (2022-01-26 01:21:26 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 0x00004a90 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\surface\gridsurf.py", line 76 in ses_surface_geometry
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\atomic\molsurf.py", line 232 in calculate_surface_geometry
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 195 in _calculate_surface
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\core\threadq.py", line 31 in run
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001d60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000055d0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\threading.py", line 312 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\queue.py", line 90 in join
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\core\threadq.py", line 64 in apply_to_list
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 162 in surface
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\std_commands\show.py", line 154 in show_surfaces
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\std_commands\show.py", line 47 in show
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897 in run
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\core\commands\run.py", line 38 in run
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\shortcuts\shortcuts.py", line 512 in run
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\shortcuts\shortcuts.py", line 569 in run_expanded_command
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\shortcuts\shortcuts.py", line 327 in run
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\shortcuts\shortcuts.py", line 408 in run_shortcut
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\shortcuts\shortcuts.py", line 390 in try_shortcut
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1334 in run_provider
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\shortcuts\__init__.py", line 52 in run_provider
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1286 in run_provider
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\toolbar\tool.py", line 205 in callback
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202201260121\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202201260121 (2022-01-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Toni/Downloads/cryosparc_P40_J182_007_volume_map_sharp.mrc

Opened cryosparc_P40_J182_007_volume_map_sharp.mrc as #1, grid size
128,128,128, pixel 1.89, shown at level 0.326, step 1, values float32  

> volume #1 level 0.1686

> surface dust #1 size 18.9

> open C:/Users/Toni/Downloads/cryosparc_P40_J190_002_volume_map_sharp.mrc

Opened cryosparc_P40_J190_002_volume_map_sharp.mrc as #2, grid size
128,128,128, pixel 1.89, shown at level 0.354, step 1, values float32  

> volume #2 level 0.1058

> close

> open 6poe

6poe title:  
Structure of ACLY in complex with CoA [more info...]  
  
Chain information for 6poe #1  
---  
Chain | Description | UniProt  
A B C D | ATP-citrate synthase | ACLY_HUMAN  
  
Non-standard residues in 6poe #1  
---  
COA — coenzyme A  
  

> color #1 #88cc55 transparency 0

> color #1 #8c5c36 transparency 0

> color #1 #88cc55 transparency 0

> color #1 #885533 transparency 0

> color #1 #5533aa transparency 0

> color #1 #53af32 transparency 0

> hide cartoons

> hide #!1 models

> select #1

31780 atoms, 32469 bonds, 8 pseudobonds, 4091 residues, 2 models selected  

> show #!1 models

> show sel surfaces

> color (#!1 & sel) #5544aaff

> color (#!1 & sel) #54af32ff

> save C:/Users/Toni/OneDrive/Desktop/p20.png width 4000 height 3171
> supersample 4 transparentBackground true

> ~select #1

4 models selected  

> set bgColor white

> set bgColor #ffffff00

> save C:/Users/Toni/OneDrive/Desktop/p20.png width 4000 height 3171
> supersample 4 transparentBackground true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting flat

> lighting full

> lighting soft

> lighting full

> lighting soft

> open 6uv5

6uv5 title:  
Structure of human ATP citrate lyase in complex with acetyl-CoA and
oxaloacetate [more info...]  
  
Chain information for 6uv5 #2  
---  
Chain | Description | UniProt  
A B C D | ATP citrate lyase | ACLY_HUMAN  
  
Non-standard residues in 6uv5 #2  
---  
ACO — acetyl coenzyme *A  
OAA — oxaloacetate ion  
  

> select #2

31871 atoms, 32552 bonds, 8 pseudobonds, 4099 residues, 2 models selected  

> hide sel atoms

> show sel surfaces


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4.dev202201260121 (2022-01-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 512.15
OpenGL renderer: NVIDIA GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: de_DE.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Book 2
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 17,092,849,664
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.10
    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: 1.33.1
    ChimeraX-AtomicLibrary: 5.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    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: 1.5.1
    ChimeraX-CommandLine: 1.2
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202201260121
    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-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: 1.1.5
    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: 2.5
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    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: 1.8
    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: 1.1
    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: 1.7.4
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16
    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: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.3
    filelock: 3.4.2
    fonttools: 4.29.0
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    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: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.0.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    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
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.24
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    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: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash computing surface

comment:2 by Tom Goddard, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed

Appears to have crashed computing molecular surfaces for PDB 6uv5. I tried that on Mac with current ChimeraX and it did not crash. Don't have an idea what caused it. The structure is 32,000 atoms, not very large.

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