Opened 4 years ago

Closed 4 years ago

#5786 closed defect (can't reproduce)

Crash in event loop

Reported by: angelica-12-02@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Eric Pettersen
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: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Current thread 0x00004fa0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 1015 in 
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py", line 194 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "D:\\\Angelica\\\Desktop\\\4T\\\Amilasa\\\MECANISMO DE
> REACCIÓN\\\mecanismo de reacción.cxs"

Log from Mon Nov 22 15:11:43 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/Angelica/Desktop/4T/Amilasa/6gxv.pdb

6gxv.pdb title:  
Amylase In complex with acarbose [more info...]  
  
Chain information for 6gxv.pdb #1  
---  
Chain | Description  
A B | A-amylase  
  
Non-standard residues in 6gxv.pdb #1  
---  
AC1 —
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-α-D-
glucopyranose (N-[4-hydroxymethyl-
cyclohexan-6-yl-1,2,3-triol]-4,6-dideoxy-4-aminoglucopyranoside)  
BGC — β-D-glucopyranose  
CA — calcium ion  
GLC — α-D-glucopyranose  
NA — sodium ion  
  

> select :AC1

84 atoms, 88 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select :BGC

48 atoms, 48 bonds, 4 residues, 1 model selected  

> select :BGC

48 atoms, 48 bonds, 4 residues, 1 model selected  

> select :CA

6 atoms, 6 residues, 1 model selected  

> hide sel atoms

> select :NA

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select :BGC

48 atoms, 48 bonds, 4 residues, 1 model selected  

> select :BGC

48 atoms, 48 bonds, 4 residues, 1 model selected  

> select :BGC

48 atoms, 48 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select :AC1

84 atoms, 88 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select :GLC

140 atoms, 142 bonds, 12 residues, 1 model selected  

> hide sel atoms

> select :AC1

84 atoms, 88 bonds, 4 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> hide sel cartoons

Drag select of 615 atoms, 962 residues, 484 bonds  

> hide sel cartoons

> select clear

Drag select of 911 atoms, 802 bonds  

> hide sel atoms

> show sel cartoons

> show sel cartoons

> select ALL

Expected an objects specifier or a keyword  

> select all

8945 atoms, 8076 bonds, 51 pseudobonds, 2079 residues, 2 models selected  

> show sel cartoons

Alignment identifier is 1  

> open D:/Angelica/Desktop/4T/Amilasa/estructuras/Amilasa-ITASSER.pdb

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

> ui tool show Matchmaker

> 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 6gxv.pdb, chain B (#1) with Amilasa-ITASSER.pdb, chain A (#2),
sequence alignment score = 315.7  
RMSD between 106 pruned atom pairs is 1.096 angstroms; (across all 402 pairs:
12.349)  
  

> select /A:4-484

10802 atoms, 10997 bonds, 962 residues, 2 models selected  

> hide sel cartoons

> select #1

8945 atoms, 8076 bonds, 51 pseudobonds, 2079 residues, 2 models selected  

> hide #!1 models

> select #2

18971 atoms, 19238 bonds, 1267 residues, 1 model selected  
Alignment identifier is 2/A  

> select #2/A:774

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

> select #2/A:774

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

> color sel red

> select #2/A:805

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

> select #2/A:805

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

> color sel red

> select #2/A:886

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

> select #2/A:886

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

> color sel red

> show sel surfaces

> select #2/A:1-1267

18971 atoms, 19238 bonds, 1267 residues, 1 model selected  

> show sel surfaces

> transparency (#!2 & sel) 90

> show sel cartoons

> set bgColor white

> view orient

> view orient

> hide sel surfaces

> select helix

5330 atoms, 5381 bonds, 487 residues, 2 models selected  

> color (#!2 & sel) orange

> select strand

3319 atoms, 3329 bonds, 320 residues, 2 models selected  

> color (#!2 & sel) light sea green

> select coil

17898 atoms, 18086 bonds, 1422 residues, 2 models selected  

> color (#!2 & sel) gray

Alignment identifier is 1  
Alignment identifier is 2/A  

> select #2/A:774

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

> select #2/A:774

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

> color (#!2 & sel) red

> select #2/A:805

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

> select #2/A:805

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

> color (#!2 & sel) red

> select #2/A:886

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

> select #2/A:886

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

> color (#!2 & sel) red

> show sel atoms

> select #2/A:774

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

> show sel atoms

> select #2/A:805

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

> show sel atoms

> save "D:/Angelica/Desktop/4T/Amilasa/MECANISMO DE REACCIÓN/mecanismo de
> reacción.cxs"

——— End of log from Mon Nov 22 15:11:43 2021 ———

opened ChimeraX session  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 3480
OS: Microsoft Windows 11 Home Single Language (Build 22000)
Memory: 8,445,366,272
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
OSLanguage: es-MX
Locale: ('es_MX', 'cp1252')
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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    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: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    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: 2.0.1
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

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

Reported by Angelica Cruz

comment:2 by Tom Goddard, 4 years ago

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

Looks like ChimeraX crashed after opening a session file

open "D:\Angelica\Desktop\4T\Amilasa\MECANISMO DEREACCIÓN\mecanismo de reacción.cxs"

It crashed in the Qt window toolkit event loop giving no clues about what caused the crash. If it always crashes when opening this file then we could probably debug it if you sent the session file.

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