Opened 4 years ago

Closed 4 years ago

#6519 closed defect (can't reproduce)

Crash running coulombic

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Surface/Binding Analysis Version:
Keywords: Cc:
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: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Current thread 0x00005d08 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\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 1VPQ

Summary of feedback from opening 1VPQ fetched from pdb  
---  
notes | Fetching compressed mmCIF 1vpq from
http://files.rcsb.org/download/1vpq.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
  
1vpq title:  
CRYSTAL STRUCTURE OF a DUF72 family protein (TM1631) FROM THERMOTOGA MARITIMA
MSB8 AT 2.20 A RESOLUTION [more info...]  
  
Chain information for 1vpq #1  
---  
Chain | Description | UniProt  
A | hypothetical protein TM1631 | Q9X1W6_THEMA  
  
Non-standard residues in 1vpq #1  
---  
SO4 — sulfate ion  
  
1vpq mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  

> close session

> open 1vqp

Summary of feedback from opening 1vqp fetched from pdb  
---  
notes | Fetching compressed mmCIF 1vqp from
http://files.rcsb.org/download/1vqp.cif  
Fetching CCD K from http://ligand-expo.rcsb.org/reports/K/K/K.cif  
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD SR from http://ligand-expo.rcsb.org/reports/S/SR/SR.cif  
Fetching CCD CD from http://ligand-expo.rcsb.org/reports/C/CD/CD.cif  
Fetching CCD DCZ from http://ligand-expo.rcsb.org/reports/D/DCZ/DCZ.cif  
Fetching CCD PPU from http://ligand-expo.rcsb.org/reports/P/PPU/PPU.cif  
Fetching CCD HFA from http://ligand-expo.rcsb.org/reports/H/HFA/HFA.cif  
Fetching CCD PO2 from http://ligand-expo.rcsb.org/reports/P/PO2/PO2.cif  
  
1vqp title:  
The structure of the transition state analogue "RAP" bound to the large
ribosomal subunit of haloarcula marismortui [more info...]  
  
Chain information for 1vqp #1  
---  
Chain | Description | UniProt  
0 | 23S ribosomal rna |  
1 | 50S ribosomal protein L37e | RL37_HALMA  
2 | 50S ribosomal protein L39e | RL39_HALMA  
3 | 50S ribosomal protein L44E | RL44_HALMA  
4 | 5'-R(*(DC)P*(DC)P*(ppu)*(lof)P*(PO2)P*ap*C*C)-3' |  
9 | 5S ribosomal RNA |  
A | 50S ribosomal protein L2P | RL2_HALMA  
B | 50S ribosomal protein L3P |  
C | 50S ribosomal protein L4E | RL4_HALMA  
D | 50S ribosomal protein L5P | RL5_HALMA  
E | 50S ribosomal protein L6P | RL6_HALMA  
F | 50S ribosomal protein L7AE | RL7A_HALMA  
G | acidic ribosomal protein P0 homolog | RLA0_HALMA  
H | 50S ribosomal protein L10E |  
I | 50S ribosomal protein L11P |  
J | 50S ribosomal protein L13P | RL13_HALMA  
K | 50S ribosomal protein L14P | RL14_HALMA  
L | 50S ribosomal protein L15P | RL15_HALMA  
M | 50S Ribosomal Protein L15E |  
N | 50S ribosomal protein L18P | RL18_HALMA  
O | 50S ribosomal protein L18e | R18E_HALMA  
P | 50S ribosomal protein L19E | RL19_HALMA  
Q | 50S ribosomal protein L21e | RL21_HALMA  
R | 50S ribosomal protein L22P | RL22_HALMA  
S | 50S ribosomal protein L23P | RL23_HALMA  
T | 50S ribosomal protein L24P | RL24_HALMA  
U | 50S ribosomal protein L24E | R24E_HALMA  
V | 50S ribosomal protein L29P | RL29_HALMA  
W | 50S ribosomal protein L30P | RL30_HALMA  
X | 50S ribosomal protein L31e | RL31_HALMA  
Y | 50S ribosomal protein L32E | RL32_HALMA  
Z | 50S ribosomal protein L37Ae |  
  

> hide

> style stick

Changed 99070 atom styles  

> show :1904-103

> hide

> show :"1903

> show :1904

> view

> show :1903

> zone :1904

> show cartoons

> delete hoh

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete solvent

> zone :1903

> show cartoons

> color bynucleotide

> color hetatom

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color byhetero

> hide cartoons

> expand

Unknown command: expand  

> show cartoons

> hide surfaces

> hide cartoons

> set bgColor white

> save C:\Users\torre\Desktop\image2.png supersample 3

> ui mousemode right label

> ui mousemode right "move label"

> save C:\Users\torre\Desktop\image3.png supersample 3

> save C:/Users/torre/Desktop/h_marismortui_50S.cxs

> select /0

59284 atoms, 66080 bonds, 3269 pseudobonds, 3017 residues, 4 models selected  

> color /A green

> color sel bynucleotide

> color rainbow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> rainbow

> color bychain

> color /A orange

> color /0 orange

> color sel bynucleotide

> color sel byhetero

> save C:\Users\torre\Desktop\image2.png supersample 3

> save C:/Users/torre/Desktop/h_marismortui_50S.cxs

> close session

> open "G:/.shortcut-targets-by-id/1mrvVMHEogMFKgxM7JV-dhOX_WVJ7ssXt/Hector
> Torres Vera (2021 - ) MCB/QE/figures/b7a_ecoli_ocuniculus.cxs"

opened ChimeraX session  

> lighting simple

> lighting soft

> lighting full

> color /a orange

> color /A green

> coulombic


===== 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 451.67
OpenGL renderer: GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GS65 Stealth 9SD
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 17,016,512,512
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_US', '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: 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-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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    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
    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
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash running coulombic

comment:2 by Eric Pettersen, 4 years ago

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