Opened 2 years ago

Closed 2 years ago

#10329 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-3.10.0-957.21.3.el7.x86_64-x86_64-with-glibc2.17
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 0x00007f9b217b2700 (most recent call first):
  File "/home/rodolpho/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/openmm/forcefields.py", line 66 in _background_load_ff
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/concurrent/futures/thread.py", line 52 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/concurrent/futures/thread.py", line 77 in _worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f9ab17e8700 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1284 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f9b77119740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> set selectionWidth 4

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/rodolpho/Projects/ycf1_pka_tom_1stmodel.pdb

ycf1_pka_tom_1stmodel.pdb title:  
Alphafold V2.0 prediction for metal resistance protein YCF1 (P39109) [more
info...]  
  
Chain information for ycf1_pka_tom_1stmodel.pdb #1  
---  
Chain | Description | UniProt  
A | metal resistance protein YCF1 | YCFI_YEAST  
  
Non-standard residues in ycf1_pka_tom_1stmodel.pdb #1  
---  
SEP — (SEP)  
TPO — (TPO)  
  

> open /home/rodolpho/Projects/isolde/AlphaFold_P39109.pdb

Chain information for AlphaFold_P39109.pdb #2  
---  
Chain | Description  
A | No description available  
  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ycf1_pka_tom_1stmodel.pdb, chain A (#1) with AlphaFold_P39109.pdb,
chain A (#2), sequence alignment score = 7797.2  
RMSD between 872 pruned atom pairs is 0.901 angstroms; (across all 1515 pairs:
5.206)  
  

> open "/home/rodolpho/Projects/phenix final
> refs/RealSpaceRefine_20/Final/ycf1_pka_valid.pdb"

Chain information for ycf1_pka_valid.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #!3 models

> hide #1 models

> open /home/rodolpho/Desktop/Maps/cryosparc_P5_J556_008_volume_map.mrc

Opened cryosparc_P5_J556_008_volume_map.mrc as #4, grid size 440,440,440,
pixel 0.822, shown at level 0.0336, step 2, values float32  

> close #4

> open "/home/rodolpho/Desktop/Paper
> Figures/cryosparc_P5_J665_006_volume_map.mrc"

Opened cryosparc_P5_J665_006_volume_map.mrc as #4, grid size 440,440,440,
pixel 0.822, shown at level 0.0378, step 2, values float32  

> hide #2 models

> show #1 models

> color #4 #00fff022 models

> set bgColor white

> volume #4 step 1

> surface dust #4 size 8.22

> volume #4 level 0.04794

> open /home/rodolpho/Desktop/Maps/cryosparc_P5_J556_008_volume_map.mrc

Opened cryosparc_P5_J556_008_volume_map.mrc as #5, grid size 440,440,440,
pixel 0.822, shown at level 0.0336, step 2, values float32  

> volume #5 color #00fff022

> volume #5 step 1

> volume #5 level 0.04606

> fitmap #2 inMap #5

Fit molecule AlphaFold_P39109.pdb (#2) to map
cryosparc_P5_J556_008_volume_map.mrc (#5) using 12061 atoms  
average map value = 0.09813, steps = 108  
shifted from previous position = 0.412  
rotated from previous position = 0.802 degrees  
atoms outside contour = 4672, contour level = 0.046058  
  
Position of AlphaFold_P39109.pdb (#2) relative to
cryosparc_P5_J556_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.30692198 0.66910367 0.67683024 182.09711253  
-0.08697159 0.72789698 -0.68014846 191.09266856  
-0.94775252 0.14988751 0.28160059 167.15506705  
Axis 0.42031159 0.82265226 -0.38285955  
Axis point 207.73288448 0.00000000 49.08633439  
Rotation angle (degrees) 80.89699992  
Shift along axis 169.74342913  
  

> hide #1 models

> show #2 models

> fitmap #1 inMap #5

Fit molecule ycf1_pka_tom_1stmodel.pdb (#1) to map
cryosparc_P5_J556_008_volume_map.mrc (#5) using 24319 atoms  
average map value = 0.08404, steps = 124  
shifted from previous position = 0.357  
rotated from previous position = 1.11 degrees  
atoms outside contour = 9998, contour level = 0.046058  
  
Position of ycf1_pka_tom_1stmodel.pdb (#1) relative to
cryosparc_P5_J556_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99994144 -0.01081267 0.00046124 1.94155859  
0.01081868 0.99981276 -0.01604353 1.12588272  
-0.00028768 0.01604758 0.99987119 -2.99013713  
Axis 0.82905459 0.01934780 0.55883285  
Axis point 0.00000000 185.49865877 68.05956155  
Rotation angle (degrees) 1.10897405  
Shift along axis -0.03954544  
  

> show #1 models

> hide #1 models

> hide #2 models

> show #!3 models

> fitmap #3 inMap #5

Fit molecule ycf1_pka_valid.pdb (#3) to map
cryosparc_P5_J556_008_volume_map.mrc (#5) using 23753 atoms  
average map value = 0.09044, steps = 84  
shifted from previous position = 0.885  
rotated from previous position = 0.678 degrees  
atoms outside contour = 8736, contour level = 0.046058  
  
Position of ycf1_pka_valid.pdb (#3) relative to
cryosparc_P5_J556_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99993840 0.00751438 0.00816920 -3.03225516  
-0.00754772 0.99996328 0.00405776 1.31724045  
-0.00813841 -0.00411917 0.99995840 1.68554959  
Axis -0.34564130 0.68932723 -0.63667893  
Axis point 274.46612764 0.00000000 335.89409951  
Rotation angle (degrees) 0.67774711  
Shift along axis 0.88292842  
  

> hide #!3 models

> show #2 models

> show #!4 models

> hide #!5 models

> color #4 #f400f4 models transparency 0

> color #4 #f400f419 models

> fitmap #2 inMap #4

Fit molecule AlphaFold_P39109.pdb (#2) to map
cryosparc_P5_J665_006_volume_map.mrc (#4) using 12061 atoms  
average map value = 0.1228, steps = 124  
shifted from previous position = 0.959  
rotated from previous position = 0.426 degrees  
atoms outside contour = 3673, contour level = 0.047938  
  
Position of AlphaFold_P39109.pdb (#2) relative to
cryosparc_P5_J665_006_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.30227004 0.66673020 0.68125154 181.96340816  
-0.08288126 0.73035895 -0.67801660 190.42400039  
-0.94961230 0.14848112 0.27602507 167.81968948  
Axis 0.41825968 0.82531939 -0.37935042  
Axis point 207.05263006 0.00000000 49.09025469  
Rotation angle (degrees) 81.12223166  
Shift along axis 169.60610789  
  

> close #1

> close #3

> close #4

> show #!5 models

> fitmap #2 inMap #5

Fit molecule AlphaFold_P39109.pdb (#2) to map
cryosparc_P5_J556_008_volume_map.mrc (#5) using 12061 atoms  
average map value = 0.09813, steps = 104  
shifted from previous position = 0.96  
rotated from previous position = 0.422 degrees  
atoms outside contour = 4672, contour level = 0.046058  
  
Position of AlphaFold_P39109.pdb (#2) relative to
cryosparc_P5_J556_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.30687206 0.66907955 0.67687671 182.09631755  
-0.08693138 0.72792279 -0.68012598 191.09367844  
-0.94777237 0.14986984 0.28154318 167.15431688  
Axis 0.42028848 0.82268040 -0.38282444  
Axis point 207.72135566 0.00000000 49.08671085  
Rotation angle (degrees) 80.89936478  
Shift along axis 169.75125025  
  

> select clear

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 222 residues in model #2 to IUPAC-IUB
standards.  
Chain information for AlphaFold_P39109.pdb  
---  
Chain | Description  
1.2/A | No description available  
  


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

Log:
> set selectionWidth 4

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 430.34
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B09
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen Threadripper 2950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G         18G         28G        331M         79G        105G
	Swap:          4.0G        1.4G        2.6G

Graphics:
	0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 Rev. A] [10de:1e87] (rev a1)	
	Subsystem: eVga.com. Corp. Device [3842:2183]	
	Kernel driver in use: nvidia
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-Clipper: 0.17.0
    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-ISOLDE: 1.3
    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, 2 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, 2 years ago

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