Crash deleting residues

[emcrae@…]

The following bug report has been submitted:
Platform:        Linux-5.8.0-59-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.
Please describe steps that led to the crash here.
Model building with ISOLDE loaded, trying to delete residues.
Fatal Python error: Aborted

Current thread 0x00007f0e42d64740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/atomic/molarray.py", line 744 in delete
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/std_commands/delete.py", line 39 in delete_atoms
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/std_commands/delete.py", line 22 in delete
  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/cmd_line/tool.py", line 164 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 318 in forward_keystroke
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/graphics.py", line 57 in event
  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: 3.3.0 NVIDIA 470.42.01
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi       8.5Gi       106Gi       447Mi        10Gi       115Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2204] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:87af]	
	Kernel driver in use: nvidia
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-Clipper: 0.16.0
    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-ISOLDE: 1.2.2
    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
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    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
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    six: 1.15.0
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    wheel: 0.36.0
    wheel-filename: 1.2.0

[Eric Pettersen]

Hi Ewan,

Thanks for reporting this problem. Can you provide any more specifics? What residues were you trying to delete. Were there anything unusual about those residues, or about the structure in general?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[emcrae@…]

Hi Eric,

I was working on a 1300nt RNA structure. I had ISOLDE open but not running and I was using the make bond command to join together 3 strands of RNA. I believe the error occurs because the make bond command renames the strands so that they are all called "B". Then the identifiers are no longer unique, in this case B913, B914 and B915 exist twice. I selected the three residues I wanted to delete with my cursor and execute "del sel" to remove them and this results in the crash.

I am pretty sure I have deleted residues with non-unique identifiers in ChimeraX before, so I am not sure what makes this specific structure crash the program.

Happy to provide the files if it is of interest or use.

Best,

Ewan K.S. McRae, PhD,
Andersen lab for Biomolecular Design
Interdisciplinary Nanoscience Center
Aarhus University, Denmark


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, July 6, 2021 10:24 PM
Cc: Ewan Kenneth Strome McRae <emcrae@inano.au.dk>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4863: Crash deleting residues

#4863: Crash deleting residues
-------------------------------+----------------------------
          Reporter:  emcrae@…  |      Owner:  Eric Pettersen
              Type:  defect    |     Status:  feedback
          Priority:  normal    |  Milestone:
         Component:  Core      |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 Hi Ewan,
         Thanks for reporting this problem.  Can you provide any more
 specifics?  What residues were you trying to delete.  Were there anything
 unusual about those residues, or about the structure in general?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4863#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Hi Ewan,

If you are willing to provide the structure, that would be helpful. A session file with the residues selected just before the "del sel" command would be fantastic if possible. You could send the mail directly to me (pett@…) so that it doesn't wind up attached to this ticket if you want the data to remain confidential. My mail can accept large attachments.

--Eric