Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6311 closed defect (fixed)

Crash computing secondary structure

Reported by: drew.parsons@… 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-5.16.0-3-amd64-x86_64-with-glibc2.33
ChimeraX Version: 1.4.dev202203030220 (2022-03-03 02:20:09 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.

Attempted to open a PDB structure (example attached).
Running on Debian unstable.



Fatal Python error: Segmentation fault

Current thread 0x00007fa8fbfe0740 (most recent call first):
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 197 in get_prop
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/atomic/ribbon.py", line 95 in _make_ribbon_graphics
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/atomic/ribbon.py", line 589 in compute_ribbons
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 650 in _create_ribbon_graphics
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 346 in update_graphics_if_needed
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1766 in _update_graphics_if_needed
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/graphics/view.py", line 271 in check_for_drawing_change
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/graphics/view.py", line 620 in drawing_bounds
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/models.py", line 688 in add
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 248 in provider_open
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 155 in _qt_safe
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax-techpreview/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/drew/SecureWork/cagliari/grants/PRIN/g-quadruplex/2lby.pdb

2lby.pdb title:  
G-quadruplex structure formed At the 5'-end of nheiii_1 element In human C-myc
promoter [more info...]  
  
Chain information for 2lby.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | DNA (5'-
D(*TP*ap*GP*GP*GP*ap*GP*GP*GP*TP*ap*GP*GP*GP*ap*GP*GP*GP*T)-3')  
  


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

Log:
UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 21.3.7
OpenGL renderer: Mesa Intel(R) UHD Graphics (CML GT2)
OpenGL vendor: Intel

Locale: en_AU.UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-xorg
XDG_SESSION_DESKTOP=gnome-xorg
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:0
Manufacturer: LENOVO
Model: 20S0CTO1WW
OS: Debian GNU/Linux unstable sid
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
Cache Size: 8192 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            23Gi       7.9Gi       1.3Gi       3.6Gi        14Gi        11Gi
	Swap:           27Gi       458Mi        26Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation CometLake-U GT2 [UHD Graphics] [8086:9b41] (rev 02)	
	Subsystem: Lenovo CometLake-U GT2 [UHD Graphics] [17aa:22b0]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    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: 1.36.2
    ChimeraX-AtomicLibrary: 6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.1
    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: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203030220
    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-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: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.2
    ChimeraX-ModelPanel: 1.3.2
    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: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.7.7
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.0
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
File attachment: 2lby.pdb

2lby.pdb​

Attachments (1)

2lby.pdb​ (506.2 KB ) - added by drew.parsons@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (6)

by drew.parsons@…, 4 years ago

Attachment: 2lby.pdb​ added

Added by email2trac

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash computing secondary structure

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Hi Drew,

Thanks for reporting this problem. I have applied a fix and the fix will be in tomorrow's build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

fix: ​https://github.com/RBVI/ChimeraX/commit/d9ba0adb0a5073b05350a72752c7430bd5fd0686

in reply to:  4 comment:3 by drew.parsons@…, 4 years ago 

Fast work, I'll give it a test.

Drew


ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> ha scritto:

in reply to:  5 ; comment:4 by drew.parsons@…, 4 years ago 

Confirming ChimeraX is now displaying the structure, not crashing.
Thanks for the fix.

Drew Parsons



ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> ha scritto:

comment:5 by Eric Pettersen, 4 years ago

Great!

--Eric

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