Opened 4 years ago

Closed 4 years ago

#4716 closed defect (duplicate)

Crash opening PDB-Dev model 65

Reported by: goddard@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Higher-Order Structure Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-73-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.

Start ChimeraX and run this command crashes after fetching the IHM data before any models are displayed.
open 65 from pdbdev
Shell reports

goddard@beetracker:~$ chimerax
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::erase: __pos (which is 18446744073709551615) > this->size() (which is 0)
Aborted (core dumped)

Fatal Python error: Aborted

Thread 0x00007fb286c2d700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 306 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 558 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 1252 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007fb28742e700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 306 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 558 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 1252 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007fb293fff700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.8/ssl.py", line 1099 in read
  File "/usr/lib/ucsf-chimerax/lib/python3.8/ssl.py", line 1241 in recv_into
  File "/usr/lib/ucsf-chimerax/lib/python3.8/socket.py", line 669 in readinto
  File "/usr/lib/ucsf-chimerax/lib/python3.8/http/client.py", line 268 in _read_status
  File "/usr/lib/ucsf-chimerax/lib/python3.8/http/client.py", line 307 in begin
  File "/usr/lib/ucsf-chimerax/lib/python3.8/http/client.py", line 1347 in getresponse
  File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 1358 in do_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 1397 in https_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 502 in _call_chain
  File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 542 in _open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 525 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/urllib/request.py", line 222 in urlopen
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/toolshed/available.py", line 47 in load
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/toolshed/__init__.py", line 459 in reload_available
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 870 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.8/threading.py", line 890 in _bootstrap

Current thread 0x00007fb339a4a740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/pdb/pdb.py", line 74 in open_pdb
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/ihm.py", line 1200 in models
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/ihm.py", line 348 in read_comparative_models
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/ihm.py", line 256 in read_starting_models
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/ihm.py", line 71 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/ihm.py", line 37 in read_ihm
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/__init__.py", line 25 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 422 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 179 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/manager.py", line 187 in open_data
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/fetch_ihm.py", line 40 in fetch_ihm
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ihm/__init__.py", line 36 in fetch
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 421 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 150 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 280 in execute
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 117 in keyPressEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 866 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.8/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: 4.6 (Core Profile) Mesa 20.2.6
OpenGL renderer: Mesa Intel(R) HD Graphics 6000 (BDW GT3)
OpenGL vendor: Intel
Manufacturer: unknown
Model: unknown
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 4 Intel(R) Core(TM) i5-5250U CPU @ 1.60GHz
Cache Size: 3072 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       1.3Gi       9.4Gi       529Mi       4.8Gi        13Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 6000 [8086:1626] (rev 09)	
	Subsystem: Intel Corporation HD Graphics 6000 [8086:2057]	
	Kernel driver in use: i915
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: 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-LinuxSupport: 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
    distro: 1.5.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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: 1.2.0

Change History (2)

comment:1 by Tom Goddard, 4 years ago

Component: Unassigned → Higher-Order Structure
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash opening PDB-Dev model 65

Same as #4713.

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed
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