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#7378 closed defect (can't reproduce)

Crash deleting structure during session close

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

Description

The following bug report has been submitted:
Platform:        Linux-5.4.0-122-generic-x86_64-with-glibc2.27
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

Current thread 0x00007f0ec60de680 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 1372 in delete
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 115 in delete
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/models.py", line 895 in close
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/models.py", line 574 in reset_state
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/session.py", line 535 in reset
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/std_commands/close.py", line 60 in close_session
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 680 in file_close_cb
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1032 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/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  

> volume showOutlineBox true

No volumes specified  

> open "/home/mbotova/Documents/MD
> simulations/N234/ensemble/7cdzArenumbered.pdb" "/home/mbotova/Documents/MD
> simulations/N234/ensemble/N_hel2_B_2_sccomp1.pdb"
> "/home/mbotova/Documents/MD
> simulations/N234/ensemble/N_hel2_A_2_sccomp1.pdb"

Summary of feedback from opening /home/mbotova/Documents/MD
simulations/N234/ensemble/N_hel2_B_2_sccomp1.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
996 messages similar to the above omitted  
  
Summary of feedback from opening /home/mbotova/Documents/MD
simulations/N234/ensemble/N_hel2_A_2_sccomp1.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
996 messages similar to the above omitted  
  
Chain information for 7cdzArenumbered.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for N_hel2_B_2_sccomp1.pdb #2  
---  
Chain | Description  
? | No description available  
  
Chain information for N_hel2_A_2_sccomp1.pdb #3  
---  
Chain | Description  
? | No description available  
  

> open "/home/mbotova/Documents/MD
> simulations/N234/ensemble/7cdzArenumbered.pdb"

Chain information for 7cdzArenumbered.pdb #4  
---  
Chain | Description  
A | No description available  
  

> matchmaker #1 to #2

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 N_hel2_B_2_sccomp1.pdb, chain (blank) (#2) with
7cdzArenumbered.pdb, chain A (#1), sequence alignment score = 575.2  
RMSD between 67 pruned atom pairs is 1.247 angstroms; (across all 128 pairs:
5.730)  
  

> matchmaker #4 to #3

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 N_hel2_A_2_sccomp1.pdb, chain (blank) (#3) with
7cdzArenumbered.pdb, chain A (#4), sequence alignment score = 575.2  
RMSD between 67 pruned atom pairs is 1.247 angstroms; (across all 128 pairs:
5.567)  
  

> select #2

3210 atoms, 3274 bonds, 419 residues, 1 model selected  

> select #2:1-167

1283 atoms, 1314 bonds, 167 residues, 1 model selected  

> delete #2:1-167

> delete #3:1-167

> delete #3:365-419

> delete #2:365-419

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #4/A

Alignment identifier is 1  

> combine #1 #2

> select #5

2500 atoms, 2556 bonds, 325 residues, 1 model selected  

> log metadata #5

The model has no metadata

> log chains #5

Chain information for combination #5  
---  
Chain | Description  
? | No description available  
A | No description available  
  

> delete #1:168-174

> delete #4:168-174

> hide #5 models

> combine #1 #2

> combine #3 #4

> select #6:167-168

15 atoms, 14 bonds, 2 residues, 1 model selected  

> style sel ball

Changed 15 atom styles  

> show sel atoms

> select #6:167-169

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #7:167-169

24 atoms, 23 bonds, 3 residues, 1 model selected  

> style sel ball

Changed 24 atom styles  

> show sel atoms

> bond #6:167@C #6:168@N reasonabld false

Expected a keyword  

> bond #6:167@C #6:168@N reasonable false

Created 1 bond  

> hide #6 models

> show #6 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> select #6

2442 atoms, 2496 bonds, 318 residues, 1 model selected  

> select #7

2442 atoms, 2495 bonds, 318 residues, 1 model selected  

> close session

> open "/home/mbotova/Documents/MD
> simulations/N234/ensemble/7cdzArenumbered.pdb" "/home/mbotova/Documents/MD
> simulations/N234/ensemble/N_hel2_B_2_sccomp1.pdb"
> "/home/mbotova/Documents/MD
> simulations/N234/ensemble/N_hel2_A_2_sccomp1.pdb"

Summary of feedback from opening /home/mbotova/Documents/MD
simulations/N234/ensemble/N_hel2_B_2_sccomp1.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
996 messages similar to the above omitted  
  
Summary of feedback from opening /home/mbotova/Documents/MD
simulations/N234/ensemble/N_hel2_A_2_sccomp1.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
996 messages similar to the above omitted  
  
Chain information for 7cdzArenumbered.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for N_hel2_B_2_sccomp1.pdb #2  
---  
Chain | Description  
? | No description available  
  
Chain information for N_hel2_A_2_sccomp1.pdb #3  
---  
Chain | Description  
? | No description available  
  

> open "/home/mbotova/Documents/MD
> simulations/N234/ensemble/7cdzArenumbered.pdb"

Chain information for 7cdzArenumbered.pdb #4  
---  
Chain | Description  
A | No description available  
  

> ui windowfill toggle

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #2 models

> show #2 models

> hide #3 models

> show #3 models

> hide #4 models

> show #4 models

> hide #1 models

> show #1 models

> hide #4 models

> hide #1 models

> show #1 models

> show #4 models

> matchmaker #1 #2

Missing required "to" argument  

> matchmaker #1 to #2

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 N_hel2_B_2_sccomp1.pdb, chain (blank) (#2) with
7cdzArenumbered.pdb, chain A (#1), sequence alignment score = 575.2  
RMSD between 67 pruned atom pairs is 1.247 angstroms; (across all 128 pairs:
5.730)  
  

> matchmaker #4 to #3

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 N_hel2_A_2_sccomp1.pdb, chain (blank) (#3) with
7cdzArenumbered.pdb, chain A (#4), sequence alignment score = 575.2  
RMSD between 67 pruned atom pairs is 1.247 angstroms; (across all 128 pairs:
5.567)  
  

> select #2

3210 atoms, 3274 bonds, 419 residues, 1 model selected  

> select #2:1-167

1283 atoms, 1314 bonds, 167 residues, 1 model selected  

> delete #2:1-167

> select #3:1-167

1283 atoms, 1314 bonds, 167 residues, 1 model selected  

> delete #3:1-167

> select #2:365-419

425 atoms, 428 bonds, 55 residues, 1 model selected  

> delete #2:365-419

> select #3:365-419

425 atoms, 428 bonds, 55 residues, 1 model selected  

> delete #3:365-419

> select #1:169-174

51 atoms, 52 bonds, 6 residues, 1 model selected  

> select #1:168-174

58 atoms, 60 bonds, 7 residues, 1 model selected  

> delete #1:168-174

> select #4:168-174

58 atoms, 60 bonds, 7 residues, 1 model selected  

> delete #4:168-174

> combine #1#2

> select #5

2442 atoms, 2495 bonds, 318 residues, 1 model selected  

> combine #4 #3

> select #6

2442 atoms, 2495 bonds, 318 residues, 1 model selected  

> bond #5:167@C #5:168@N

Created 1 bond  

> hide #2 models

> hide #1 models

> select #5:167-168

15 atoms, 15 bonds, 2 residues, 1 model selected  

> style sel ball

Changed 15 atom styles  

> show sel atoms

> select #5:166-168

22 atoms, 22 bonds, 3 residues, 1 model selected  

> style sel ball

Changed 22 atom styles  

> show sel atoms

> select up

549 atoms, 557 bonds, 76 residues, 1 model selected  

> select up

2442 atoms, 2496 bonds, 318 residues, 1 model selected  

> select down

549 atoms, 557 bonds, 76 residues, 1 model selected  

> select down

22 atoms, 22 bonds, 3 residues, 1 model selected  

> select down

22 atoms, 22 bonds, 3 residues, 1 model selected  

> bond #5:167@C #5:168@N reasonable false

Created 0 bonds  

> style sel ball

Changed 22 atom styles  

> show sel atoms

> bond #6:167@C #5:168@N reasonable false

Cannot bond atoms in different molecules  

> select #6:167-169

24 atoms, 23 bonds, 3 residues, 1 model selected  

> style sel ball

Changed 24 atom styles  

> show sel atoms

> bond #6:167@C #5:168@N reasonable false

Cannot bond atoms in different molecules  

> bond #6:167@C #6:168@N reasonable false

Created 1 bond  

> hide #4 models

> hide #3 models

> save "/home/mbotova/Documents/MD simulations/N234/ensemble/struct2.pdb"
> models #5-6

> open "/home/mbotova/Documents/MD simulations/N234/ensemble/struct10.pdb"

Chain information for struct10.pdb #7  
---  
Chain | Description  
A B | No description available  
  

> hide #5 models

> hide #6 models

> hide #7 models

> show #6 models

> show #5 models

> select /A

9206 atoms, 9418 bonds, 1196 residues, 5 models selected  

> hide #6 models

> show #6 models

> setattr #5/A r chain_id B

Assigning chain_id attribute to 318 items  
Cannot set attribute 'chain_id' to 'B'  

> setattr #5/A c chain_id B

Assigning chain_id attribute to 1 item  

> select /A

6764 atoms, 6922 bonds, 878 residues, 4 models selected  

> combine #5 #6

> select /A

9206 atoms, 9418 bonds, 1196 residues, 5 models selected  

> select /B

7326 atoms, 7488 bonds, 954 residues, 3 models selected  

> save "/home/mbotova/Documents/MD simulations/N234/ensemble/struct2.pdb"
> models #8

> open "/home/mbotova/Documents/MD simulations/N234/ensemble/struct10.pdb"

Chain information for struct10.pdb #9  
---  
Chain | Description  
A B | No description available  
  

> hide #8 models

> show #8 models

> hide #6 models

> hide #5 models

> select #8

4884 atoms, 4992 bonds, 636 residues, 1 model selected  

> hide #9 models

> save "/home/mbotova/Documents/MD simulations/N234/ensemble/2.cxs"

FYI: command is replacing existing command: "build modify"  
FYI: command is replacing existing command: "build start"  
FYI: command is replacing existing command: "bond"  
FYI: command is replacing existing command: "~bond"  
FYI: command is replacing existing command: "bond length"  

> 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: 4.6 (Core Profile) Mesa 20.0.8
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: Dell Inc.
Model: OptiPlex 5070
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz
Cache Size: 9216 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        5.5G        4.7G        2.6G        5.3G        7.0G
	Swap:           31G        826M         31G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e92]	
	Subsystem: Dell Device [1028:092f]	
	Kernel driver in use: i915
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: 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-LinuxSupport: 1.0
    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
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    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
    line-profiler: 3.3.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Core
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash deleting structure during session close

comment:2 by Eric Pettersen, 3 years ago

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

Not enough info to reproduce. Could well already be fixed.

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