Crash after hiding atomic model, Windows

[yen-li.li@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202109251824 (2021-09-25 18:24:47 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x800706ba

Thread 0x0000327c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002708 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\weakref.py", line 573 in __init__
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\site-packages\chimerax\atomic\molarray.py", line 1577 in remove_deleted_pointers
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\site-packages\chimerax\atomic\molarray.py", line 123 in __init__
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\site-packages\chimerax\core\commands\atomspec.py", line 480 in _check
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\site-packages\grako\contexts.py", line 683 in _choice
  File "C:\Program Files\ChimeraX 1.3.dev202109251824\bin\lib\site-packages\chimerax\atomic\molarray.py", line 1577 in remove_deleted_pointers
Windows fatal exception: access violation

Windows fatal exception: access violation

Fatal Python error: Segmentation fault

Windows fatal exception: access violation

===== Log before crash start =====
> open E:\Krios\20210423\csrelion\6221\coot\csJ245rsr86-coot-2.pdb format pdb

Chain information for csJ245rsr86-coot-2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide atoms

> show cartoons

> open "E:/temp/EM data/PDB/rcmA3G_AF2/rcmA3G_AF2.pdb"

Chain information for rcmA3G_AF2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> matchmaker #2 to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker csJ245rsr86-coot-2.pdb, chain A (#1) with rcmA3G_AF2.pdb, chain A
(#2), sequence alignment score = 1736.4  
RMSD between 181 pruned atom pairs is 1.401 angstroms; (across all 383 pairs:
3.526)  
  

> color bychain

> color #2 gold

> open "E:/temp/EM data/PDB/AF-Q9HC16-F1-model_v1.pdb"

AF-Q9HC16-F1-model_v1.pdb title:  
Alphafold V2.0 prediction for DNA DC->du-editing enzyme apobec-3G (Q9HC16)
[more info...]  
  
Chain information for AF-Q9HC16-F1-model_v1.pdb #3  
---  
Chain | Description | UniProt  
A | DNA DC->du-editing enzyme apobec-3G | ABC3G_HUMAN  
  

> matchmaker #3 to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker csJ245rsr86-coot-2.pdb, chain A (#1) with
AF-Q9HC16-F1-model_v1.pdb, chain A (#3), sequence alignment score = 2106.2  
RMSD between 366 pruned atom pairs is 0.902 angstroms; (across all 384 pairs:
1.247)  
  

> hide #!1 models

> show #!1 models

> hide #3 models

> select #1/A:128-130

38 atoms, 38 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 38 atom styles  

> show sel atoms

> color sel byhetero

> select clear

> select #2:128-130

48 atoms, 48 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 48 atom styles  

> color sel byhetero

> show sel atoms

> select clear

> set bgColor white

> graphics silhouettes true

> open 6p59 format mmcif fromDatabase pdb

6p59 title:  
Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex [more info...]  
  
Chain information for 6p59 #4  
---  
Chain | Description | UniProt  
A C | Core-binding factor subunit β | PEBB_HUMAN  
B F | Virion infectivity factor | E1ANT9_SIV  
D W | Elongin-B | ELOB_HUMAN  
E Z | Elongin-C | ELOC_HUMAN  
  
Non-standard residues in 6p59 #4  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MES — 2-(N-morpholino)-ethanesulfonic acid  
ZN — zinc ion  
  
6p59 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete #4/C,F,W,Z

> matchmaker #4/B to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker csJ245rsr86-coot-2.pdb, chain B (#1) with 6p59, chain B (#4),
sequence alignment score = 435  
RMSD between 117 pruned atom pairs is 0.832 angstroms; (across all 167 pairs:
9.970)  
  

> hide #2#!1,4 atoms

> show #2#!1,4 cartoons

> select #2:128-130

48 atoms, 48 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 48 atom styles  

> show sel atoms

> select #1/A:128-130

38 atoms, 38 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 38 atom styles  

> color sel byhetero

> hide #2 models

> show #2 models

> hide #!1 models

> select #4/B:86

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> show sel atoms

> color sel byhetero

> show #!1 models

> hide #2 models

> select #1/B:83

17 atoms, 16 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 17 atom styles  

> show sel atoms

> color sel byhetero

> hide #!4 models

> show #2 models

> hide #2 models

> show #2 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> open E:/Krios/20210423/csrelion/6221/phenix/csJ245_denmod_map.ccp4

Opened csJ245_denmod_map.ccp4 as #5, grid size 185,198,138, pixel 0.835, shown
at level 0.491, step 1, values float32  

> transparency 50

> hide #!1 models


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

Log:
UCSF ChimeraX version: 1.3.dev202109251824 (2021-09-25)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 471.68
OpenGL renderer: NVIDIA GeForce RTX 2060 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 34,261,569,536
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('zh_TW', 'cp950')
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: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.1
    ChimeraX-AtomicLibrary: 4.1.4
    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
    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: 2.1
    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.dev202109251824
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    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: 2.1.1
    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: 2.0.1
    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
    ChimeraX-ModelPanel: 1.2
    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: 2.6.3
    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
    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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.4
    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
    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
    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: 0.10.0
    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: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    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: 4.8.1
    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: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    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: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    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: 2.1.0
    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: 5.1.0
    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

[Eric Pettersen]

Reported by Yen-Li Li

Last logged command is "hide #!1 models". I don't see how line 480 in atomspec.py can invoke the Collection constructor.

[Tom Goddard]

Not enough information in the crash report to debug this.

The Python tracebacks are from the previous non-fatal "Windows fatal exception: code 0x800706ba" which is "Error code 0x800706BA indicates that the remote procedure call (RPC) server is unavailable." After that there in an access violation and segmentation fault and no Python traceback.

The log shows opening some PDB files, running matchmaker, deleting some chains, running matchmaker, opening a ccp4 map, then hiding a PDB model and it crashes.