Opened 3 years ago

Closed 3 years ago

#8648 closed defect (can't reproduce)

Crash in event loop

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-67-generic-x86_64-with-glibc2.31
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.
Fatal Python error: Segmentation fault

Current thread 0x00007f13ca207740 (most recent call first):
  File "/soft/UCSF-ChimeraX/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/soft/UCSF-ChimeraX/chimerax-1.3/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/soft/UCSF-ChimeraX/chimerax-1.3/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/soft/UCSF-ChimeraX/chimerax-1.3/lib/python3.9/runpy.py", line 87 in _run_code
  File "/soft/UCSF-ChimeraX/chimerax-1.3/lib/python3.9/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 /home/valentovalucka/Documents/KONFERENCE/Nove_hrady_23/baseplate.cxc

> close session

> camera ortho

> set bgColor white

> lighting shadows true

> graphics silhouettes true

> lighting soft

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/baseplate_composite_map_540px.mrc

Opened baseplate_composite_map_540px.mrc as #1, grid size 540,540,540, pixel
0.834, shown at level 8.18, step 4, values float32  

> volume #1 style surface step 1 showOutlineBox false

> volume #1 step 1

> volume #1 level 8

> volume #1 color #B2B2B2

> volume #1 transparency 0

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp49_DIT/RealSpaceRefine_4_FINAL_DIT/dit_tal_bpup-
> coot-5_real_space_refined_004_chainC_DIT_trimer.pdb

Chain information for dit_tal_bpup-
coot-5_real_space_refined_004_chainC_DIT_trimer.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> color #2 #204A87

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp50_BPUP/RealSpaceRefine_1_FINAL_BpUp_TAL/gp50_BpUp_trimer.pdb

Chain information for gp50_BpUp_trimer.pdb #3  
---  
Chain | Description  
A B I | No description available  
  

> color #3 #A40000

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp53_TAL/RealSpaceRefine_1_FINAL_BpUp_TAL/gp53_TAL_trimer.pdb

Chain information for gp53_TAL_trimer.pdb #4  
---  
Chain | Description  
A B H | No description available  
  

> color #4 #C4A000

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp54_RBP/RealSpaceRefine_4_FINAL/gp54_one_chain_rejoined-
> coot-1_trimer_real_space_refined_004_trimer_tripod.pdb

Chain information for gp54_one_chain_rejoined-
coot-1_trimer_real_space_refined_004_trimer_tripod.pdb #5  
---  
Chain | Description  
A B C D E F G H I | No description available  
  

> color #5 #5C3566

> hide atoms

> show cartoons

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/TailFibres/RealSpaceRefine_2_FINAL/TF_trimer_gp47_gp48_heterodimers.pdb

Chain information for TF_trimer_gp47_gp48_heterodimers.pdb #6  
---  
Chain | Description  
A C D G H K L M N | No description available  
B E F I J O P Q R | No description available  
  

> color #6 #69a742

> hide atoms

> show cartoons

> select #6/A,C,D,G,H,K,L,M,N

43488 atoms, 44154 bonds, 2853 residues, 1 model selected  

> color sel #D3D7CF

> select clear

> ui tool show "Hide Dust"

> surface dust #1 size 2.6

executed baseplate.cxc  

> turn x

> hide #2 models

> hide #3 models

> hide #6 models

> hide #5 models

> hide #4 models

> open /home/valentovalucka/Documents/KONFERENCE/Nove_hrady_23/baseplate.cxc

> close session

> camera ortho

> set bgColor white

> lighting shadows true

> graphics silhouettes true

> lighting soft

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/baseplate_composite_map_540px.mrc

Opened baseplate_composite_map_540px.mrc as #1, grid size 540,540,540, pixel
0.834, shown at level 8.18, step 4, values float32  

> volume #1 style surface step 1 showOutlineBox false

> volume #1 step 1

> volume #1 level 8

> volume #1 color #B2B2B2

> volume #1 transparency 0

> ui tool show "Hide Dust"

> surface dust #1 size 2.6

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp49_DIT/RealSpaceRefine_4_FINAL_DIT/dit_tal_bpup-
> coot-5_real_space_refined_004_chainC_DIT_trimer.pdb

Chain information for dit_tal_bpup-
coot-5_real_space_refined_004_chainC_DIT_trimer.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> color #2 #204A87

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp50_BPUP/RealSpaceRefine_1_FINAL_BpUp_TAL/gp50_BpUp_trimer.pdb

Chain information for gp50_BpUp_trimer.pdb #3  
---  
Chain | Description  
A B I | No description available  
  

> color #3 #A40000

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp53_TAL/RealSpaceRefine_1_FINAL_BpUp_TAL/gp53_TAL_trimer.pdb

Chain information for gp53_TAL_trimer.pdb #4  
---  
Chain | Description  
A B H | No description available  
  

> color #4 #C4A000

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/Baseplate/gp54_RBP/RealSpaceRefine_4_FINAL/gp54_one_chain_rejoined-
> coot-1_trimer_real_space_refined_004_trimer_tripod.pdb

Chain information for gp54_one_chain_rejoined-
coot-1_trimer_real_space_refined_004_trimer_tripod.pdb #5  
---  
Chain | Description  
A B C D E F G H I | No description available  
  

> color #5 #5C3566

> hide atoms

> show cartoons

> open
> /home/valentovalucka/brno14/jbd30_4/ModelBuilding/TailFibres/RealSpaceRefine_2_FINAL/TF_trimer_gp47_gp48_heterodimers.pdb

Chain information for TF_trimer_gp47_gp48_heterodimers.pdb #6  
---  
Chain | Description  
A C D G H K L M N | No description available  
B E F I J O P Q R | No description available  
  

> color #6 #69a742

> hide atoms

> show cartoons

> select #6/A,C,D,G,H,K,L,M,N

43488 atoms, 44154 bonds, 2853 residues, 1 model selected  

> color sel #D3D7CF

> select clear

> hide #2,3,4,5,6

executed baseplate.cxc  


===== 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 510.108.03
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: Super Server
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD EPYC 7313P 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          251Gi       4.8Gi       245Gi        83Mi       1.6Gi       244Gi
	Swap:            0B          0B          0B

Graphics:
	44:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	DeviceName: ASPEED Video AST2500	
	Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:1b95]
Locale: ('en_US', 'UTF-8')
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-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: 2.0.4
    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
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    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
    line-profiler: 3.3.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop

comment:2 by Eric Pettersen, 3 years ago

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