Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#6744 closed defect (duplicate)

Crash processing events or recording movie

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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-10-10.0.22000
ChimeraX Version: 1.4.dev202204270129 (2022-04-27 01:29:17 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x00003610 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\threading.py", line 1297 in run
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00007364 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\ui\gui.py", line 849 in rapid_access_shown
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\ui\gui.py", line 852 in _check_rapid_access
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\triggerset.py", line 134 in invoke
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\triggerset.py", line 217 in _activate
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\triggerset.py", line 186 in activate
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\triggerset.py", line 354 in activate_trigger
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\models.py", line 677 in add
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\open_command\cmd.py", line 248 in provider_open
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897 in run
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\open_command\cmd.py", line 118 in cmd_open
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897 in run
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\commands\run.py", line 38 in run
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\scripting.py", line 173 in _run_commands
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\scripting.py", line 160 in open_command_script
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core_formats\__init__.py", line 37 in open
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\open_command\cmd.py", line 428 in remember_data_format
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\open_command\cmd.py", line 440 in collated_open
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\open_command\cmd.py", line 193 in provider_open
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897 in run
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\open_command\cmd.py", line 118 in cmd_open
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2897 in run
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\chimerax\core\commands\run.py", line 38 in run
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\ChimeraX_main.py", line 846 in init
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202204270129\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202204270129 (2022-04-27)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\windo\\\Documents\\\Alex's Shared Resources\\\Uni\\\Year
> 3\\\Semester 2\\\Structures of destruction\\\Video Project Folder\\\Spinning
> NPC-C1 with focus on loops at the ened\\\Script.cxc"

> open 5F18

5f18 title:  
Structural basis of Ebola virus entry: viral glycoprotein bound to its
endosomal receptor Niemann-Pick C1 [more info...]  
  
Chain information for 5f18 #1  
---  
Chain | Description | UniProt  
A | Niemann-Pick C1 protein | NPC1_HUMAN  
  

> cd "C:/Users/windo/Documents/Alex's Shared Resources/Uni/Year 3/Semester
> 2/Structures of destruction/Video Project Folder/Spinning NPC-C1 with focus
> on loops at the ened"

Current working directory is: C:\Users\windo\Documents\Alex's Shared
Resources\Uni\Year 3\Semester 2\Structures of destruction\Video Project
Folder\Spinning NPC-C1 with focus on loops at the ened  

> wait 60

> set bgColor white

> select /A

1969 atoms, 1850 bonds, 398 residues, 1 model selected  

> rainbow

> setattr :126-128 res ss_type 0

Assigning ss_type attribute to 3 items  

> setattr :133-135 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> turn y 90

> turn x 90

> turn z 80

> view

> view name center

> zoom 2

> move y -20

> turn y 90

> move x -8

> view name loops-b-two

> view center

> movie record size 1920, 1080

> turn y 2 600

> wait 600


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

Log:
UCSF ChimeraX version: 1.4.dev202204270129 (2022-04-27)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\windo\\\Documents\\\Alex's Shared Resources\\\Uni\\\Year
> 3\\\Semester 2\\\Structures of destruction\\\Video Project Folder\\\Spinning
> NPC-C1 with focus on loops at the ened\\\Script.cxc"

> open 5F18

5f18 title:  
Structural basis of Ebola virus entry: viral glycoprotein bound to its
endosomal receptor Niemann-Pick C1 [more info...]  
  
Chain information for 5f18 #1  
---  
Chain | Description | UniProt  
A | Niemann-Pick C1 protein | NPC1_HUMAN  
  

> cd "C:/Users/windo/Documents/Alex's Shared Resources/Uni/Year 3/Semester
> 2/Structures of destruction/Video Project Folder/Spinning NPC-C1 with focus
> on loops at the ened"

Current working directory is: C:\Users\windo\Documents\Alex's Shared
Resources\Uni\Year 3\Semester 2\Structures of destruction\Video Project
Folder\Spinning NPC-C1 with focus on loops at the ened  

> wait 60

> set bgColor white

> select /A

1969 atoms, 1850 bonds, 398 residues, 1 model selected  

> rainbow

> setattr :126-128 res ss_type 0

Assigning ss_type attribute to 3 items  

> setattr :133-135 res ss_type 0

Assigning ss_type attribute to 3 items  

> select clear

> turn y -60

> turn z 120

> turn x 40

> view

> view name center

> zoom 2.5

> turn x 180

> move y -20

> view name loops-b-two

> view center

> movie record size 1920, 1080

> turn y 2 600

> wait 600

> view loops-b-two 75

> wait 75

[Repeated 1 time(s)]

> movie encode spinning_NPC_C1_with_focus_on_loops_at_end.mp4

Movie saved to spinning_NPC_C1_with_focus_on_loops_at_end.mp4  
  

> view loops-b-two

> movie record size 1920, 1080

> wait 250

> movie encode loop_still_frame_10_secs.mp4

Movie saved to loop_still_frame_10_secs.mp4  
  
executed Script.cxc  




OpenGL version: 3.3.0 NVIDIA 512.59
OpenGL renderer: NVIDIA GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Razer
Model: Blade 15 Mid 2019-Base
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 17,073,299,456
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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: 1.38.2
    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: 2.2.3
    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.dev202204270129
    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-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
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.5
    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
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0a1
    grako: 3.16.5
    h5py: 3.6.0
    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
    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
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.8
    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
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    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
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash processing events or recording movie

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Apparently reproducible for somebody!

comment:3 by Tom Goddard, 3 years ago

Again crashed in Qt sub-eventloop processing.

Note: See TracTickets for help on using tickets.