Opened 4 years ago

Last modified 4 years ago

#6342 assigned defect

Crash registering webcam command during session save

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.13.0-30-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3.dev202109020559 (2021-09-02 05:59:02 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f3359557740 (most recent call first):
  File "", line 228 in _call_with_frames_removed
  File "", line 1173 in create_module
  File "", line 565 in module_from_spec
  File "", line 666 in _load_unlocked
  File "", line 986 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/Qt/QtMultimedia.py", line 4 in 
  File "", line 228 in _call_with_frames_removed
  File "", line 850 in exec_module
  File "", line 680 in _load_unlocked
  File "", line 986 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/webcam/webcam.py", line 424 in 
  File "", line 228 in _call_with_frames_removed
  File "", line 850 in exec_module
  File "", line 680 in _load_unlocked
  File "", line 986 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "", line 228 in _call_with_frames_removed
  File "", line 1058 in _handle_fromlist
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/webcam/__init__.py", line 20 in register_command
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1271 in register_command
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 312 in _register_cmd
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 302 in cb
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2105 in call
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2174 in lazy_register
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 3432 in find_aliases
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 3442 in find_aliases
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 3448 in list_aliases
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/session.py", line 392 in take_snapshot
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/session.py", line 281 in process
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/session.py", line 260 in discovery
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/session.py", line 608 in save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/session.py", line 878 in save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 84 in save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 89 in provider_save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 51 in display
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 116 in 
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/ChimeraX_main.py", line 882 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/ChimeraX_main.py", line 1031 in 
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3.dev202109020559 (2021-09-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/fulbabu/Documents/JAK_KINASE/jak1_socs1/analysis/run1/2p/pdb/final-2p.pdb

Chain information for final-2p.pdb #1  
---  
Chain | Description  
? | No description available  
  

> set bgColor white

> lighting soft

> select ::name="ADP"

42 atoms, 44 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select ::name="MG"

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select /?:58

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

229 atoms, 228 bonds, 13 residues, 1 model selected  

> select up

6512 atoms, 6585 bonds, 406 residues, 1 model selected  

> hide sel atoms

> select clear

> select /?:325

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

> select up

120 atoms, 120 bonds, 8 residues, 1 model selected  

> select up

6512 atoms, 6585 bonds, 406 residues, 1 model selected  

> select down

120 atoms, 120 bonds, 8 residues, 1 model selected  

> select :1-286

4611 atoms, 4662 bonds, 286 residues, 1 model selected  

> color sel light sea green

> select :290-406

1857 atoms, 1879 bonds, 117 residues, 1 model selected  

> color sel hot pink

> select clear

> ui tool show H-Bonds

> hbonds color #73d216 radius 0.085 dashes 7 interModel false intraModel false
> saltOnly true intraMol false intraRes false reveal true

0 hydrogen bonds found  

> hbonds color #73d216 radius 0.085 dashes 7 interModel false intraModel false
> saltOnly true intraMol false reveal true

0 hydrogen bonds found  

> hbonds color #73d216 radius 0.085 dashes 7 interModel false intraModel false
> saltOnly true reveal true

0 hydrogen bonds found  

> hbonds color #73d216 radius 0.085 dashes 7 interModel false saltOnly true
> reveal true

44 hydrogen bonds found  

> hbonds color #73d216 radius 0.085 dashes 7 saltOnly true reveal true

44 hydrogen bonds found  

> hbonds color #73d216 radius 0.085 dashes 7 saltOnly true reveal true

44 hydrogen bonds found  

> color byhetero

> ui tool show H-Bonds

> hbonds color #010e13 radius 0.085 dashes 7 saltOnly true reveal true

44 hydrogen bonds found  

> hbonds color #010e13 radius 0.085 dashes 7 saltOnly true reveal true

44 hydrogen bonds found  

> select /?:184@CG

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /?:57@CE

1 atom, 1 residue, 1 model selected  

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /?:60@OE2

1 atom, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /?:172@CG

1 atom, 1 residue, 1 model selected  

> select add /?:174@CZ

2 atoms, 2 residues, 1 model selected  

> select add /?:168@P

3 atoms, 1 bond, 3 residues, 1 model selected  

> select up

7 atoms, 2 bonds, 5 residues, 1 model selected  

> select up

106 atoms, 102 bonds, 5 residues, 1 model selected  

> select add /?:167@CZ

107 atoms, 102 bonds, 6 residues, 1 model selected  

> select add /?:165@CD

108 atoms, 102 bonds, 7 residues, 1 model selected  

> select up

152 atoms, 148 bonds, 7 residues, 1 model selected  

> select ~sel

6360 atoms, 6437 bonds, 35 pseudobonds, 399 residues, 2 models selected  

> transparency sel 80 ribbons

> transparency sel 60 ribbons

> select clear

> save /home/fulbabu/Documents/JAK_KINASE/jak1_socs1/analysis/data/new-
> data/2p/hb-2p.png width 3546 height 2250 supersample 4 transparentBackground
> true

> save /home/fulbabu/Documents/JAK_KINASE/jak1_socs1/analysis/data/new-
> data/2p/map.cxs includeMaps true


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

Log:
UCSF ChimeraX version: 1.3.dev202109020559 (2021-09-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 21.0.3
OpenGL renderer: Mesa Intel(R) HD Graphics 630 (KBL GT2)
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 7050
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       3.4Gi       382Mi       1.4Gi        11Gi        10Gi
	Swap:         2.0Gi       2.0Mi       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:5912] (rev 04)	
	DeviceName: Intel HD Graphics	
	Subsystem: Dell HD Graphics 630 [1028:07a1]
Locale: ('en_IN', 'ISO8859-1')
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: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29
    ChimeraX-AtomicLibrary: 4.1.4
    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: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109020559
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 2.1.1
    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-LinuxSupport: 1.0
    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: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1
    ChimeraX-ModelPanel: 1.1
    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: 2.6.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    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: 2.4.2
    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
    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: 1.12
    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
    cxservices: 1.0.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.10.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    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: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash registering webcam command during session save

comment:2 by Tom Goddard, 4 years ago

Crash importing QtMultimedia. Saving a session should not try to register every aliased ChimeraX command. Saving a session where a user will lose work when it fails is the worst time to be trying to needlessly register all these ChimeraX commands. There is another ticket reporting this, and one asking that session save not try to register the unused commands.

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