glClear access violation

[trevor.sewell@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18363
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.
Windows fatal exception: access violation

Current thread 0x00008cb4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 1166 in draw_background
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\camera.py", line 184 in draw_background
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 215 in _draw_scene
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 165 in draw
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 73 in draw_new_frame
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 139 in _redraw_timer_callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 111 in make_current
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 490 in make_current
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\statusbar.py", line 143 in status
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\statusbar.py", line 84 in _expose_event
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 2184 in _release
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 2164 in delete
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 1895 in _mask_framebuffer
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 1837 in set_outline_mask
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 237 in _draw_scene
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 165 in draw
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 465 in image_rgba
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 415 in image
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 231 in models_image
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 173 in capture_image
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 85 in capture_thumbnails_cb
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 68 in remember_file
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 224 in remember_file
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\session.py", line 914 in save
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core_formats\__init__.py", line 84 in save
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\save_command\cmd.py", line 89 in provider_save
  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\save_command\cmd.py", line 75 in cmd_save
  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\save_command\dialog.py", line 51 in display
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\save_command\dialog.py", line 127 in show_save_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\save_command\dialog.py", line 116 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
Windows fatal exception: access violation

Current thread 0x00008cb4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 111 in make_current
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 490 in make_current
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\statusbar.py", line 143 in status
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\statusbar.py", line 84 in _expose_event
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 2184 in _release
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 2164 in delete
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 1895 in _mask_framebuffer
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\opengl.py", line 1837 in set_outline_mask
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 237 in _draw_scene
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 165 in draw
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 465 in image_rgba
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 415 in image
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 231 in models_image
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 173 in capture_image
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 85 in capture_thumbnails_cb
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 68 in remember_file
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\filehistory.py", line 224 in remember_file
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\session.py", line 914 in save
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core_formats\__init__.py", line 84 in save
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\save_command\cmd.py", line 89 in provider_save
  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\save_command\cmd.py", line 75 in cmd_save
  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\save_command\dialog.py", line 51 in display
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\save_command\dialog.py", line 127 in show_save_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\save_command\dialog.py", line 116 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
> D:/CynD-Q86R/All_chains/RealSpaceRefine_3/Q86R-corrected_model1-coot-2.pdb

Chain information for Q86R-corrected_model1-coot-2.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R | No description available  
  

> addh

Summary of feedback from adding hydrogens to Q86R-corrected_model1-coot-2.pdb
#1  
---  
notes | No usable SEQRES records for Q86R-corrected_model1-coot-2.pdb (#1)
chain A; guessing termini instead  
No usable SEQRES records for Q86R-corrected_model1-coot-2.pdb (#1) chain B;
guessing termini instead  
No usable SEQRES records for Q86R-corrected_model1-coot-2.pdb (#1) chain C;
guessing termini instead  
No usable SEQRES records for Q86R-corrected_model1-coot-2.pdb (#1) chain D;
guessing termini instead  
No usable SEQRES records for Q86R-corrected_model1-coot-2.pdb (#1) chain E;
guessing termini instead  
13 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A SER 3, /B SER 3, /C SER
3, /D SER 3, /E SER 3, /F SER 3, /G SER 3, /H SER 3, /I SER 3, /J SER 3, /K
SER 3, /L SER 3, /M SER 3, /N SER 3, /O SER 3, /P SER 3, /Q SER 3, /R SER 3  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ILE 319, /B ILE 319, /C
ILE 319, /D ILE 319, /E ILE 319, /F ILE 319, /G ILE 319, /H ILE 319, /I ILE
319, /J ILE 319, /K ILE 319, /L ILE 319, /M ILE 319, /N ILE 319, /O ILE 319,
/P ILE 319, /Q ILE 319, /R ILE 319  
3654 hydrogen bonds  
/A ILE 319 is not terminus, removing H atom from 'C'  
/B ILE 319 is not terminus, removing H atom from 'C'  
/C ILE 319 is not terminus, removing H atom from 'C'  
/D ILE 319 is not terminus, removing H atom from 'C'  
/E ILE 319 is not terminus, removing H atom from 'C'  
13 messages similar to the above omitted  
43758 hydrogens added  
  

> style stick

Changed 89172 atom styles  

> style stick

Changed 89172 atom styles  

> select :80-90, 65-70

5490 atoms, 5526 bonds, 306 residues, 1 model selected  

> open D:/CynD-Q86R/All_chains/Map4_D1_3_15.mrc

Opened Map4_D1_3_15.mrc as #2, grid size 300,300,300, pixel 1.05, shown at
level 0.0246, step 2, values float32  

> volume #2 step 1

> volume #2 style mesh

> ui tool show ISOLDE

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 10.1 - if installed, please make sure this is
on your library path before starting ChimeraX.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 774 residues in model #1 to IUPAC-IUB
standards.  
Chain information for Q86R-corrected_model1-coot-2.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M
1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Done loading forcefield  
Opened Map4_D1_3_15.mrc as #1.1.1.1, grid size 300,300,300, pixel 1.05, shown
at step 1, values float32  

> clipper spotlight radius 13.00

> clipper spotlight radius 14.00

> clipper spotlight radius 15.00

> clipper spotlight radius 16.00

> clipper spotlight radius 17.00

> clipper spotlight radius 18.00

> clipper spotlight radius 19.00

> clipper spotlight radius 20.00

> clipper spotlight radius 21.00

> clipper spotlight radius 22.00

> clipper spotlight radius 23.00

> clipper spotlight radius 24.00

> clipper spotlight radius 25.00

> clipper spotlight radius 26.00

> volume #1.1.1.1 level 0.02929

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 46 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "D:/CynD-Q86R/All_chains/Q86R refinement.cxs"

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
exception: access violation reading 0x0000000000000008  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\view.py", line 215, in _draw_scene  
camera.draw_background(vnum, r)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\camera.py", line 184, in draw_background  
render.draw_background()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1166, in draw_background  
GL.glClear(flags)  
OSError: exception: access violation reading 0x0000000000000008  
  


===== 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
OpenGL renderer: Quadro FX 580/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Enterprise (Build 18363)
Memory: 34,300,129,280
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
OSLanguage: en-US
Locale: ('en_ZA', '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-Clipper: 0.17.0
    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-ISOLDE: 1.3
    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

[Tom Goddard]

This crash looks like some multi-thread problem either caused by ISOLDE or by ChimeraX save dialog.

The traceback shows it releasing an OpenGL framebuffer and during that a window expose event is fired. That should not be possible. Then during drawing for that expose event the QOpenGLContext.makeCurrent() call is made and during it a redraw timer fires. Again that should not be possible. It appears that Qt events are dispatching, maybe in another thread. The Python faulthandler output shows these all in a single thread, but I suspect that faulthandler only knows about Python threads, and a C++ thread might show Python calls mixed in the same stack trace as we see here.

The Qt save dialog starts sub-eventloop processing that could somehow be causing this although I have never seen it before. Possibly some ISOLDE threads ran amuck.

It is also baffling how two "access violation" fatal errors are reported when the first should have killed the process.