Crash after swapaa

[jhebda@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.14393
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00002c6c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00000118 (most recent call first):
  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 1hbo format mmcif fromDatabase pdb

Summary of feedback from opening 1hbo fetched from pdb  
---  
warning | Start and end residues of struct_conf "HELX_P93" are in different
chains near line 1914  
  
1hbo title:  
Methyl-coenzyme M reductase MCR-RED1-silent [more info...]  
  
Non-standard residues in 1hbo #1  
---  
CL — chloride ion  
COM — 1-thioethanesulfonic acid  
F43 — factor 430  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NA — sodium ion  
TP7 — Coenzyme B (7-mercaptoheptanoylthreoninephosphate)  
ZN — zinc ion  
  

> close session

> open 1hho format mmcif fromDatabase pdb

1hho title:  
Structure of human oxyhaemoglobin At 2.1 angstroms resolution [more info...]  
  
Non-standard residues in 1hho #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
OXY — oxygen molecule  
PO4 — phosphate ion  
  
1hho mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sym #1 assembly 1

> view

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2.1/A #2.2/A

Alignment identifier is 1  

> select #1/A:92 #2.1/A:92 #2.2/A:92

33 atoms, 30 bonds, 3 residues, 3 models selected  

> select #1/A:92 #2.1/A:92 #2.2/A:92

33 atoms, 30 bonds, 3 residues, 3 models selected  
Seqview [ID: 1] region 3 chains [92] RMSD: 26.331  
  

> show sel & #!2.1-2 atoms

> hide sel & #!2.1-2 atoms

> show sel & #!2.1-2 atoms

> select #2.1/A:92@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> select sel @ show sel & #!2.1-2 atoms

> select up

246 atoms, 244 bonds, 31 residues, 3 models selected  

> show sel & #!2.1-2 atoms

> select #2.1/A:92@CZ

1 atom, 1 residue, 1 model selected  

> select #2.1/A:92@CZ

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> center

Unknown command: center  

> pivot

Unknown command: pivot  

> view sel

> ui tool show "Side View"

> ui tool show Rotamers

> swapaa interactive sel LEU rotLib Dunbrack

1hho #2.1/A ARG 92: phi 55.5, psi 54.6 trans  
Changed 45 bond radii  

> swapaa #2.1/A:92 LEU criteria 3 rotLib Dunbrack

Using Dunbrack library  
1hho #2.1/A ARG 92: phi 55.5, psi 54.6 trans  
Applying LEU rotamer (chi angles: -79.0 68.0) to 1hho #2.1/A LEU 92  


===== 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  

> open 1hho format mmcif fromDatabase pdb

1hho title:  
Structure of human oxyhaemoglobin At 2.1 angstroms resolution [more info...]  
  
Chain information for 1hho #1  
---  
Chain | Description | UniProt  
A | hemoglobin A (oxy) (α chain) | HBA_HUMAN  
B | hemoglobin A (oxy) (β chain) | HBB_HUMAN  
  
Non-standard residues in 1hho #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
OXY — oxygen molecule  
PO4 — phosphate ion  
  
1hho mmCIF Assemblies  
---  
1| author_defined_assembly  
  




OpenGL version: 3.3.0 - Build 22.20.16.4799
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 5590
OS: Microsoft Windows 10 Enterprise 2016 LTSB (Build 14393)
Memory: 17,032,478,720
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
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
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    Jinja2: 3.0.1
    jupyter-client: 6.1.12
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    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
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    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
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    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
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    RandomWords: 0.3.0
    requests: 2.26.0
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    suds-jurko: 0.6
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    tinyarray: 1.2.3
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    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Hi Jim,

Thanks for reporting this problem. It looks like it crashed after you swapped in a rotamer. Did it crash right afterward or were you doing something further when it crashed?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab