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#6208 closed defect (fixed)

Crash deleting structure

Reported by:	rhloring@…	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:        Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
I was checking the error message I was getting if I tried to bond two peptides together without first combining the chains into a single model.  I was using the pdbs for the alphafold version of mu-conotoxin and mu-conotoxin from the pdb database.  After successfully bonding, I closed the session and instead of just closing, the session aborted.
Fatal Python error: Aborted

Current thread 0x00002bf0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\molobject.py", line 1372 in delete
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 115 in delete
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\models.py", line 895 in close
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\models.py", line 574 in reset_state
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\session.py", line 535 in reset
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\close.py", line 60 in close_session
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2856 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 680 in file_close_cb
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1032 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\rhlor\Dropbox\Research\ChimeraX data\Bond AF-mu CTX to mu-
> CTX.cxs" format session

opened ChimeraX session  

> close session

> open "C:/Users/rhlor/Dropbox/Research/ChimeraX data/AF-mu conotoxin
> P0C349.pdb"

> open "C:/Users/rhlor/Dropbox/Research/ChimeraX data/Mu-Conotoxin P0C349.pdb"

Chain information for Mu-Conotoxin P0C349.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select #2

316 atoms, 319 bonds, 22 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected atoms"

> undo

> view

> select #2

316 atoms, 319 bonds, 22 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.42999,-0.24761,0.86822,9.7454,-0.0605,0.9674,0.24593,0.97289,-0.9008,0.053219,-0.43095,0.83888

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.42999,-0.24761,0.86822,-5.8423,-0.0605,0.9674,0.24593,-1.0157,-0.9008,0.053219,-0.43095,2.4714

> select clear

> select #2

316 atoms, 319 bonds, 22 residues, 1 model selected  

> view matrix models
> #2,-0.42999,-0.24761,0.86822,-7.7728,-0.0605,0.9674,0.24593,-1.2128,-0.9008,0.053219,-0.43095,3.3709

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.29694,-0.24409,0.92317,-8.3191,-0.0095519,0.96749,0.25273,-1.462,-0.95485,0.06623,-0.28962,4.052

> view matrix models
> #2,-0.68656,-0.29476,0.66464,-7.0137,-0.0044679,0.91583,0.40154,-1.1133,-0.72706,0.27271,-0.63009,2.0526

> view matrix models
> #2,-0.70316,0.2295,0.67297,-6.5625,0.23158,0.96879,-0.088415,-3.6669,-0.67226,0.093677,-0.73437,1.3614

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.70316,0.2295,0.67297,-7.0729,0.23158,0.96879,-0.088415,2.8512,-0.67226,0.093677,-0.73437,2.8934

> select clear

> ui mousemode right "translate selected models"

> select #1

164 atoms, 167 bonds, 22 residues, 1 model selected  

> ~select #1

Nothing selected  

> select #2

316 atoms, 319 bonds, 22 residues, 1 model selected  

> view matrix models
> #2,-0.70316,0.2295,0.67297,-6.003,0.23158,0.96879,-0.088415,0.10785,-0.67226,0.093677,-0.73437,5.2027

> view matrix models
> #2,-0.70316,0.2295,0.67297,-5.4082,0.23158,0.96879,-0.088415,1.2332,-0.67226,0.093677,-0.73437,7.3988

> view matrix models
> #2,-0.70316,0.2295,0.67297,-5.2213,0.23158,0.96879,-0.088415,1.9393,-0.67226,0.093677,-0.73437,7.0284

> bond #2/A:22@C #1/A:1@N reasonable false

Cannot bond atoms in different molecules  

> combine #1 #2

Remapping chain ID 'A' in Mu-Conotoxin P0C349.pdb #2 to 'B'  

> close #1-2

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 3/A  

> sequence chain /B

Alignment identifier is 3/B  

> select /A:22

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:22

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /B:1

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select /B:1

26 atoms, 25 bonds, 1 residue, 1 model selected  

> bond #3/A:22@C #3/B:1@N reasonable false

Created 1 bond  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 3/A  

> select /A:22

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:1,22

55 atoms, 52 bonds, 4 residues, 1 model selected  

> select /A:22

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:1,22

55 atoms, 52 bonds, 4 residues, 1 model selected  

> close session


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 13-7378
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 8,453,287,936
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz
OSLanguage: en-US
Locale: ('en_US', '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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    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: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    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
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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-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: 1.1
    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-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1
File attachment: Mu-Conotoxin P0C349.pdb

Mu-Conotoxin P0C349.pdb

Attachments (1)

Mu-Conotoxin P0C349.pdb (24.8 KB ) - added by rhloring@… 4 years ago.: Added by email2trac

Download all attachments as: .zip

Change History (5)

by rhloring@…, 4 years ago

Attachment:	Mu-Conotoxin P0C349.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 deleting structure

Reported by Ralph Loring

comment:2 by Eric Pettersen, 4 years ago

Platform:	→ all
Project:	→ ChimeraX

I am able to reproduce this.

comment:3 by Eric Pettersen, 4 years ago

Simpler recipe:

open 1a0m
del :nh2
seq chain /A ; seq chain /B
bond /A:16@c /B:1@n reas f
close

comment:4 by Eric Pettersen, 3 years ago

Resolution:	→ fixed
Status:	accepted → closed

This no longer reproduces in the current ChimeraX, so other changes must have fixed this as well.

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