Crash computing ribbons

[cesar.menor@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
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.
Fatal Python error: Aborted

Thread 0x00007014 (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
Fatal Python error: Aborted

Current thread 0x0000694c (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 229 in _get_polymer_spline
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 70 in _make_ribbon_graphics
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 588 in compute_ribbons
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py", line 557 in _create_ribbon_graphics
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py", line 300 in update_graphics_if_needed
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py", line 1581 in _update_graphics_if_needed
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 130 in invoke
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 213 in _activate
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 182 in activate
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 350 in activate_trigger
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\view.py", line 269 in check_for_drawing_change
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 65 in draw_new_frame
  File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 138 in _redraw_timer_callback
  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.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 516.94
OpenGL renderer: NVIDIA GeForce GTX 960/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MICRO-STAR INTERNATIONAL CO., LTD
Model: MS-B08911
OS: Microsoft Windows 10 Home (Build 19044)
Memory: 8,514,162,688
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4460S CPU @ 2.90GHz
OSLanguage: es-ES
Locale: ('es_ES', '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
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    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[pett]

Reported by Cesar Menor-Salvan

[Tom Goddard]

ChimeraX crashed trying to show a ribbon depiction of a molecule. If you can provide the molecule file (e.g. PDB) and it repeatedly crashes I could look at why. My guess would be there is something bad about the data, like atoms exactly on top of each other. Another suggestion is to update to current ChimeraX 1.5, although I don't think anything in the ribbon computation code has changed.

[cesar.menor@…]

Hi Tom,

Probably the crash was due to the enormous size of the file and the limitations of memory of the old system I used. The PDB is 7Y5E

thank you!

Cesar






César Menor-Salván

Associate Professor of Biochemistry
Departamento de Biología de Sistemas-Facultad de Medicina
Instituto de Investigación Química "Andrés M. del Río”
Universidad de Alcalá

Campus Científico-Tecnológico

28805  Alcalá de Henares (Madrid)
Spain


Affiliated Researcher

NSF-NASA Center for Chemical Evolution

Georgia Institute of Technology
315 Ferst Drive NW
Atlanta GA 30332-0363 USA

"La burocracia estrangula, la informalidad libera. Una atmósfera informal supone una ventaja competitiva."

-Jack Welch

"La cuestión más persistente y urgente en nuestras vidas es: ¿qué estás haciendo por los demás?"
-Martin Luther King Jr.

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Saturday, February 4, 2023 2:11 AM
Cc: Menor Salvan César Ángel <cesar.menor@uah.es>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8435: Crash computing ribbons

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.

#8435: Crash computing ribbons
------------------------------------+-------------------------
          Reporter:  cesar.menor@…  |      Owner:  Tom Goddard
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Depiction      |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------

Comment (by Tom Goddard):

 ChimeraX crashed trying to show a ribbon depiction of a molecule.  If you
 can provide the molecule file (e.g. PDB) and it repeatedly crashes I could
 look at why.  My guess would be there is something bad about the data,
 like atoms exactly on top of each other.  Another suggestion is to update
 to current ChimeraX 1.5, although I don't think anything in the ribbon
 computation code has changed.

--
Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8435%23comment%3A2&data=05%7C01%7Ccesar.menor%40uah.es%7Cca80a5744a7f4f532fff08db064cb293%7Cced2c5527d1f4731aa3a2f0ec9629e26%7C1%7C0%7C638110698715219372%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0207GVzT9oHIM7c%2B80Wr61NqZnsOK1W%2Bp8fHiwAg8sg%3D&reserved=0>
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ChimeraX Issue Tracker

[Tom Goddard]

That 7y5e PDB model is a monster with 1.2 million atoms and 150,000 residues. But ribbons show fine for me in ChimeraX 1.5 on Windows and Mac. Maybe it will work for you if you update ChimeraX.

I was surprised how long it took to compute the ribbons, about 30 seconds, while larger structures such as 3j3q at 2.4 million atoms and 300,000 atoms took only 6 seconds. I will investigate why it takes so long to compute the ribbons for 7y5e.

[Tom Goddard]

I see the ribbons take only 4 seconds to compute the second time. I made a ticket #8446 to see why it is so slow the first time (​https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8446).