Opened 21 months ago

Closed 21 months ago

#14634 closed defect (can't reproduce)

Crash selecting aromatic rings

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.7.5-arch1-1-x86_64-with-glibc2.39
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
selected aromatic rings in structure 4CBY
Fatal Python error: Segmentation fault

Current thread 0x000078ea53dd8740 (most recent call first):
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/chem_group/support.py", line 29 in call_c_plus_plus
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/chem_group/chem_group.py", line 95 in find_aro_amines
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/chem_group/chem_group.py", line 218 in find_group
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/chem_group/chem_group.py", line 228 in select
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/chem_group/chem_group.py", line 235 in 
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 346 in selector_cb
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2488 in _parse_arg
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2629 in _process_positional_arguments
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2853 in run
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1581 in select_by_mode
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1785 in 
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/opt/chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/opt/chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/opt/chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> set bgColor white

> lighting gentle

> graphics silhouettes true color black width 2 depthJump 0.005

> select all

Nothing selected  

> color sel white

> color sel byhetero

> cartoon hide sel

> select ligand

Nothing selected  

> color sel dim gray

> color sel byhetero

UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Show Sequence Viewer"

> undo

> open
> /home/alex1/home/alex_neu/Downloads/emboss_needle-I20240226-091014-0072-8378997-p1m-aln.txt

Unrecognized file suffix '.txt'  

> open
> /home/alex1/home/alex_neu/Downloads/emboss_needle-I20240226-091014-0072-8378997-p1m-out.txt

Unrecognized file suffix '.txt'  

> open
> /home/alex1/home/alex_neu/Downloads/emboss_needle-I20240226-091014-0072-8378997-p1m.aln

Cannot open files: Syntax error in ALN file
'emboss_needle-I20240226-091014-0072-8378997-p1m.aln': First non-blank line
does not start with 'CLUSTAL'  

> open
> /home/alex1/home/alex_neu/Downloads/emboss_needle-I20240226-091014-0072-8378997-p1m.out

Install the SEQCROW bundle to open "ORCA output file" format files.  
Opener for format 'ORCA output file' is not installed; see log for more info  

> open
> /home/alex1/home/alex_neu/Downloads/emboss_needle-I20240226-091014-0072-8378997-p1m.fasta

Summary of feedback from opening
/home/alex1/home/alex_neu/Downloads/emboss_needle-I20240226-091014-0072-8378997-p1m.fasta  
---  
notes | Alignment identifier is
emboss_needle-I20240226-091014-0072-8378997-p1m.fasta  
Showing conservation header ("seq_conservation" residue attribute) for
alignment emboss_needle-I20240226-091014-0072-8378997-p1m.fasta  
  
Opened 2 sequences from emboss_needle-I20240226-091014-0072-8378997-p1m.fasta  

> open PDB:4CBY format mmcif fromDatabase pdb

4cby title:  
Design, synthesis, and biological evaluation of potent and selective Class IIa
HDAC inhibitors as a potential therapy for Huntington's disease [more info...]  
  
Chain information for 4cby #1  
---  
Chain | Description | UniProt  
A B C D | HISTONE DEACETYLASE 4 | HDAC4_HUMAN 648-1033  
  
Non-standard residues in 4cby #1  
---  
KEE — (1R,2R,3R)-2-[4-(1,3-oxazol-5-yl)phenyl]-N-oxidanyl-3-phenyl-
cyclopropane-1-carboxamide  
NA — sodium ion  
ZN — zinc ion  
  
4cby mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> select /A

2873 atoms, 2914 bonds, 20 pseudobonds, 407 residues, 2 models selected  

> select ~sel

8562 atoms, 8682 bonds, 62 pseudobonds, 1227 residues, 2 models selected  

> delete sel

> select /A:677

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel

> select /A:799

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel

> select /A:800

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel

> select /A:974

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel

> select /A:973

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel

> select clear

> select /A:974

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel

> select /A:972

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:972

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:975

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel

> select /A:676

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel

> select /A:974

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:975

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:976

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel

> select /A:677

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:676

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select /A:812

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> set bgColor white

> lighting gentle

> graphics silhouettes true color black width 2 depthJump 0.005

> select all

Nothing selected  

> color sel white

> color sel byhetero

> cartoon hide sel

> select ligand

Nothing selected  

> color sel dim gray

> color sel byhetero

UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 24.0.1-arch1.1
OpenGL renderer: AMD Radeon RX 5700 XT (radeonsi, navi10, LLVM 16.0.6, DRM 3.57, 6.7.5-arch1-1)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd
Model: MS-7C02
OS: EndeavourOS rolling rolling
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 AMD Ryzen 5 3600 6-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi        10Gi       4.1Gi       113Mi       1.8Gi       5.4Gi
	Swap:           15Gi       3.4Gi        12Gi

Graphics:
	28:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Navi 10 [Radeon RX 5600 OEM/5600 XT / 5700/5700 XT] [1002:731f] (rev c1)	
	Subsystem: Tul Corporation / PowerColor AXRX 5700 XT 8GBD6-3DHE/OC [PowerColor Red Devil Radeon RX 5700 XT] [148c:2398]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 21 months ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash selecting aromatic rings

comment:2 by Eric Pettersen, 21 months ago

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