Graphics errors after selection clear, macOS display scale confusion

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.4 (2021-05-14 07:23:00 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs format
> session

Log from Thu Jan 27 10:27:18 2022UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Jody/Teaching/NucleicAcids_2022/434repressor.cif

434repressor.cif title:  
Structure of the amino-terminal domain of phage 434 repressor At 2.0 angstroms
resolution [more info...]  
  
Chain information for 434repressor.cif #1  
---  
Chain | Description  
A | repressor protein ci  
  

> show target ab

> open /Users/Jody/Downloads/1r69.cif

1r69.cif title:  
Structure of the amino-terminal domain of phage 434 repressor At 2.0 angstroms
resolution [more info...]  
  
Chain information for 1r69.cif #2  
---  
Chain | Description  
A | repressor protein ci  
  

> sequence chain #2/A

Alignment identifier is 2/A  

> set bgColor white

> open /Users/Jody/Teaching/NucleicAcids_2022/434DNAcomplex.cif

434DNAcomplex.cif title:  
Recognition of A DNA operator by the repressor of phage 434. A view At high
resolution [more info...]  
  
Chain information for 434DNAcomplex.cif #3  
---  
Chain | Description  
A | DNA (5'-D(*ap*ap*GP*TP*ap*CP*ap*ap*ap*CP*TP*TP*TP*CP*TP*TP*G
P*TP*ap*T)-3')  
B | DNA (5'-D(*TP*ap*TP*ap*CP*ap*ap*GP*ap*ap*ap*GP*TP*TP*TP*GP*T
P*ap*CP*T)-3')  
L R | 434 repressor  
  

> select #3

1826 atoms, 1888 bonds, 43 pseudobonds, 210 residues, 2 models selected  

> ~select #3

Nothing selected  

> hide #!3 models

> ui mousemode right zoom

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> open /Users/Jody/Downloads/1tro.cif

Summary of feedback from opening /Users/Jody/Downloads/1tro.cif  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "TRP" near line 5644  
  
1tro.cif title:  
Crystal structure of TRP repressor operator complex At atomic resolution [more
info...]  
  
Chain information for 1tro.cif #4  
---  
Chain | Description  
A C E G | protein (TRP repressor)  
I J K L | DNA (5'-D(*TP*GP*TP*ap*CP*TP*ap*GP*TP*TP*ap*ap*CP*TP*ap*GP*T
P*ap*C)-3')  
  
1tro.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide #2 models

> hide #1 models

> style #4 stick

Changed 5373 atom styles  

> select #4/A#4/C#4/E#4/G

3539 atoms, 3305 bonds, 687 residues, 1 model selected  

> cartoon sel

> select nucleic-acid

2358 atoms, 2640 bonds, 128 pseudobonds, 116 residues, 4 models selected  

> color (#!4 & sel) dark gray

> color (#!4 & sel) #ffcc66ff

> select clear

> select ::name="HOH"

684 atoms, 684 residues, 4 models selected  

> hide #!4 models

> open /Users/Jody/Downloads/2nll.cif

Summary of feedback from opening /Users/Jody/Downloads/2nll.cif  
---  
note | Fetching CCD 5IU from http://ligand-expo.rcsb.org/reports/5/5IU/5IU.cif  
  
2nll.cif title:  
Retinoid X receptor-thyroid hormone receptor DNA-binding domain heterodimer
bound to thyroid response element DNA [more info...]  
  
Chain information for 2nll.cif #5  
---  
Chain | Description  
A | protein (retinoic acid receptor)  
B | protein (thyroid hormone receptor)  
C | DNA (5'-D(*CP*ap*GP*GP*TP*CP*ap*TP*TP*(5IU)P*CP*ap*GP*GP*TP*CP*ap*G)-3')  
D | DNA (5'-D(*CP*TP*GP*ap*CP*CP*TP*GP*ap*ap*ap*TP*GP*ap*CP*CP*T P*G)-3')  
  
Non-standard residues in 2nll.cif #5  
---  
ZN — zinc ion  
  

> hide #!5 models

> save /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs

——— End of log from Thu Jan 27 10:27:18 2022 ———

opened ChimeraX session  

> open /Users/Jody/Downloads/1par.cif

1par.cif title:  
Dna recognition by β-sheets In the arc repressor-operator crystal structure
[more info...]  
  
Chain information for 1par.cif #6  
---  
Chain | Description  
A B C D | protein (arc repressor)  
E | DNA (5'-D(*TP*ap*TP*ap*GP*TP*ap*GP*ap*GP*TP*GP*CP*TP*TP*CP*T
P*ap*TP*CP*ap*T)- 3')  
F | DNA (5'-D(*ap*ap*TP*GP*ap*TP*ap*GP*ap*ap*GP*CP*ap*CP*TP*CP*T
P*ap*CP*TP*ap*T)- 3')  
  

> surface #6

> transparency #6 50

> hide #6 target a

> cartoon #6

> save /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs

> select nucleic-acid

3986 atoms, 4464 bonds, 215 pseudobonds, 196 residues, 8 models selected  

> ui tool show "Color Actions"

> color sel goldenrod

> color sel dark goldenrod

> color sel peru

> transparency (#!6 & sel) 50

> select clear

> open /Users/Jody/Downloads/1vtl.cif

Summary of feedback from opening /Users/Jody/Downloads/1vtl.cif  
---  
warnings | Atom H5T is not in the residue template for DG /A:201  
Atom H5T is not in the residue template for DT /B:301  
Atom H5T is not in the residue template for DG /C:401  
Atom H5T is not in the residue template for DT /D:501  
  
1vtl.cif title:  
Co-crystal structure of TBP recognizing the minor groove of A tata element
[more info...]  
  
Chain information for 1vtl.cif #7  
---  
Chain | Description  
A C | DNA (5'-D(*GP*CP*TP*ap*TP*ap*ap*ap*ap*GP*GP*GP*CP*A)-3')  
B D | DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*ap*TP*ap*GP*C)-3')  
E F | tata binding protein (TBP)  
  
1vtl.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #7/C:401-414

321 atoms, 358 bonds, 14 residues, 1 model selected  

> close #7

> open /Users/Jody/Downloads/1vtl.cif

Summary of feedback from opening /Users/Jody/Downloads/1vtl.cif  
---  
warnings | Atom H5T is not in the residue template for DG /A:201  
Atom H5T is not in the residue template for DT /B:301  
Atom H5T is not in the residue template for DG /C:401  
Atom H5T is not in the residue template for DT /D:501  
  
1vtl.cif title:  
Co-crystal structure of TBP recognizing the minor groove of A tata element
[more info...]  
  
Chain information for 1vtl.cif #7  
---  
Chain | Description  
A C | DNA (5'-D(*GP*CP*TP*ap*TP*ap*ap*ap*ap*GP*GP*GP*CP*A)-3')  
B D | DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*ap*TP*ap*GP*C)-3')  
E F | tata binding protein (TBP)  
  
1vtl.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select nucleic-acid

5238 atoms, 5852 bonds, 283 pseudobonds, 252 residues, 10 models selected  

> ui tool show "Color Actions"

> color sel peru

> select

18071 atoms, 17881 bonds, 299 pseudobonds, 2627 residues, 13 models selected  

> surface (#!6-7 & sel)

> transparency (#!6-7 & sel) 50

> hide (#!6-7 & sel) target a

> cartoon (#!6-7 & sel)

> select clear

> save /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs

> ui tool show "Show Sequence Viewer"

> sequence chain #7/E #7/F

Alignment identifier is 1  

> select #7/E-F:57

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select #7/E-F:57

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select #7/E-F:74

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select #7/E-F:74

24 atoms, 24 bonds, 2 residues, 1 model selected  

> show (#!7 & sel) target ab

> style (#!7 & sel) stick

Changed 24 atom styles  

> color (#!7 & sel) red

> select #7/E-F:57

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select #7/E-F:57

24 atoms, 24 bonds, 2 residues, 1 model selected  

> show (#!7 & sel) target ab

> style (#!7 & sel) stick

Changed 24 atom styles  

> color (#!7 & sel) red

> select nucleic-acid

5238 atoms, 5852 bonds, 283 pseudobonds, 252 residues, 10 models selected  

> nucleotides (#!6-7 & sel) stubs

> show (#!6-7 & sel) target ab

> select clear

> save /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs

> hide #7.7 models

> show #7.7 models

> hide #7.7 models

> show #7.7 models

> hide #7.6 models

> hide #7.5 models

> show #7.5 models

> hide #7.4 models

> show #7.4 models

> hide #7.3 models

> hide #7.2 models

> select #7/F

1797 atoms, 1827 bonds, 186 residues, 1 model selected  

> select #7/E

1783 atoms, 1813 bonds, 186 residues, 1 model selected  

> cartoon hide (#!7 & sel)

> hide (#!7 & sel) target a

> select #6/F

458 atoms, 503 bonds, 32 residues, 1 model selected  

> select #7/A

321 atoms, 358 bonds, 14 residues, 1 model selected  

> cartoon hide (#!7 & sel)

> hide (#!7 & sel) target a

> select #7/B

305 atoms, 336 bonds, 14 residues, 1 model selected  

> cartoon hide (#!7 & sel)

> hide (#!7 & sel) target a

> save /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs

> select #7/E-F:29

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

> select #7/E-F:29

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

> show (#!7 & sel) target ab

> style (#!7 & sel) stick

Changed 16 atom styles  

> color (#!7 & sel) red

> select #7/E-F:80

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

> select #7/E-F:80

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

> select #7/E-F:72

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

> select #7/E-F:72

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

> select #7/E-F:72,80

34 atoms, 30 bonds, 4 residues, 1 model selected  

> show (#!7 & sel) target ab

> style (#!7 & sel) stick

Changed 34 atom styles  

> color (#!7 & sel) red

> select #7/E-F:29

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

> select #7/E-F:29

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

> select #7/E-F:27

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #7/E-F:27

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #7/E-F:29

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

> select #7/E-F:29

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

> select #7/E-F:27,29

38 atoms, 34 bonds, 4 residues, 1 model selected  

> select #7/E-F:27,29,117

60 atoms, 54 bonds, 6 residues, 1 model selected  

> show (#!7 & sel) target ab

> style (#!7 & sel) stick

Changed 60 atom styles  

> color (#!7 & sel) red

> select #7/E

1783 atoms, 1813 bonds, 186 residues, 1 model selected  

> hide (#!7 & sel) target a

> save /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs

> select #7/E-F:119

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

> select #7/E-F:119

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

> select #7/E-F:119,173

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select #7/E-F:119,163,173

52 atoms, 46 bonds, 6 residues, 1 model selected  

> select #7/E-F:119,163,171,173

68 atoms, 60 bonds, 8 residues, 1 model selected  

> select #7/E-F:119,148,163,171,173

92 atoms, 84 bonds, 10 residues, 1 model selected  

> select #7/E-F:74,119,148,163,171,173

116 atoms, 108 bonds, 12 residues, 1 model selected  

> show (#!7 & sel) target ab

> style (#!7 & sel) stick

Changed 116 atom styles  

> color (#!7 & sel) red

> select #7/E

1783 atoms, 1813 bonds, 186 residues, 1 model selected  

> hide (#!7 & sel) target a

> ui mousemode right zoom

> select #7/C

321 atoms, 358 bonds, 14 residues, 1 model selected  

> surface hidePatches (#!7 & sel)

> select #7/D

305 atoms, 336 bonds, 14 residues, 1 model selected  

> surface hidePatches (#!7 & sel)

> save /Users/Jody/Teaching/NucleicAcids_2022/DNA_proteincomplexes.cxs

> ui mousemode right pivot

> ui tool show "Side View"

> select

18071 atoms, 17881 bonds, 299 pseudobonds, 2627 residues, 14 models selected  

> surface hidePatches (#!6-7 & sel)

> select clear

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent  
self.render()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/sideview/tool.py", line 276, in render  
self.view.draw()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 213, in _draw_scene  
camera.draw_background(vnum, r)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/camera.py", line 184, in draw_background  
render.draw_background()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 82, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 148, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 82, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 148, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
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.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 213, in _draw_scene  
camera.draw_background(vnum, r)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/camera.py", line 184, in draw_background  
render.draw_background()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/sideview/tool.py", line 112, in _redraw  
self.render()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/sideview/tool.py", line 276, in render  
self.view.draw()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 213, in _draw_scene  
camera.draw_background(vnum, r)  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/camera.py", line 184, in draw_background  
render.draw_background()  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
Error processing trigger "frame drawn":  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60000658ed90>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60000658ed90>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x60000658ed90>
contents scale of 1 - updating layer to match.  




OpenGL version: 4.1 ATI-4.6.21
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.6.2 (20G314)
      Kernel Version: Darwin 20.6.0
      Time since boot: 7 days 16:04

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.4
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.0
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

[Tom Goddard]

OpenGL errors in glClear(). Mac laptop with Intel and AMD GPUs. Crash showed one screen, but I suspect a second screen may have been removed leading to the crash since their are warnings in the Log from Qt suggesting trouble deciding whether ChimeraX was using a retina (display scale 2) or non-retina (display scale 1) screen.

"Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60000658ed90> contents scale of 2 - updating layer to match."