glClear: invalid framebuffer operation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/adastra/Library/CloudStorage/Dropbox/ekim_nimigeanlab/2022 EK
> propofol manuscript/CB-Dock2-PFL-poc7-zoom2.cxs"

Log from Thu Jul 21 19:12:32 2022UCSF ChimeraX version: 1.4.dev202112082248
(2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/adastra/Desktop/CB-Dock2-PFL-poc7-zoom.cxs

Log from Thu Jul 21 18:36:30 2022 Startup Errors  
---  
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warning | Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 484, in get_module  
m = importlib.import_module(self.package_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py",
line 127, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "/Users/adastra/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>  
__version__ = _version()  
File "/Users/adastra/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 886, in require  
needed = self.resolve(parse_requirements(requirements))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 777, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.4.dev202112082248
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-Core~=1.3rc202112010000'), {'ChimeraX-
ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 359, in initialize  
api = self._get_api(session.logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 503, in _get_api  
m = self.get_module()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 486, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-Core 1.4.dev202112082248
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages), Requirement.parse('ChimeraX-Core~=1.3rc202112010000'), {'ChimeraX-
ISOLDE'})  
  
UCSF ChimeraX version: 1.4.dev202112082248 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/adastra/Downloads/21jul08_HCN1_PFL_out_7.-6.3.complex.pdb

Summary of feedback from opening
/Users/adastra/Downloads/21jul08_HCN1_PFL_out_7.-6.3.complex.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK The PDB FILE IS CREATED BY CY's PROGRAM CurvatureSurface AT Fri Jul 22
06:00:07 2022  
  
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  
9 messages similar to the above omitted  
  
Chain information for 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> set bgColor white

> lighting soft

> graphics silhouettes true

> color #1 white transparency 0

> select /?:1@@serial_number=1

1 atom, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> color #1 #ff7e79 transparency 0

> color #1 white transparency 0

> select clear

> select /?:1@@serial_number=1

1 atom, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> color #1 #ff7e79 transparency 0

> select clear

> ui mousemode right select

> color #1 white transparency 0

> select /?:1@@serial_number=1

1 atom, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel dark salmon

> color sel salmon

> color sel light coral

> select H

1 atom, 1 residue, 1 model selected  

> delete sel

> select /B:305

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /B:302

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

> select add /B:306

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select add /B:309

30 atoms, 26 bonds, 4 residues, 1 model selected  

> select add /B:356

38 atoms, 33 bonds, 5 residues, 1 model selected  

> select add /B:357

46 atoms, 40 bonds, 6 residues, 1 model selected  

> select add /B:382

50 atoms, 43 bonds, 7 residues, 1 model selected  

> select add /B:386

62 atoms, 55 bonds, 8 residues, 1 model selected  

> select add /B:389

73 atoms, 66 bonds, 9 residues, 1 model selected  

> select add /C:384

80 atoms, 72 bonds, 10 residues, 1 model selected  

> select add /C:383

85 atoms, 76 bonds, 11 residues, 1 model selected  

> select add /C:380

93 atoms, 83 bonds, 12 residues, 1 model selected  

> show sel atoms

> ui tool show "Color Actions"

> color sel light slate gray

> color sel byhetero

> ui mousemode right distance

> select /?:1@O

1 atom, 1 residue, 1 model selected  

> select add /B:305@SD

2 atoms, 2 residues, 1 model selected  

> ui mousemode right distance

> select /?:1@O

1 atom, 1 residue, 1 model selected  

> select add /B:305@SD

2 atoms, 2 residues, 1 model selected  

> ui mousemode right distance

[Repeated 1 time(s)]

> ui mousemode right select

> ui tool show Distances

> distance /?:1@O /B:305@SD

Distance between /? UNL 1 O and /B MET 305 SD: 3.980Å  

> distance style decimalPlaces 2

[Repeated 2 time(s)]

> distance style decimalPlaces 1

[Repeated 2 time(s)]

> distance style decimalPlaces 2

[Repeated 2 time(s)]

> distance style decimalPlaces 1

[Repeated 2 time(s)]

> distance style color black

[Repeated 2 time(s)]

> distance style color #fffb00

[Repeated 2 time(s)]

> select clear

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> hide sel cartoons

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> hide sel cartoons

> select /B:386

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

> select add /C:384

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

> select add /B:309

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

> select add /B:356

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

> ui tool show "Color Actions"

> color sel light slate gray

> color sel slate gray

> color sel light slate gray

> select clear

> ui tool show "Side View"

> ~distance /?:1@O /B:305@SD

> select /B:305

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel light slate gray

> select clear

> select /?:1@@serial_number=1

1 atom, 1 residue, 1 model selected  

> select up

13 atoms, 13 bonds, 1 residue, 1 model selected  

> size sel atomRadius 0.5

Changed 13 atom radii  

> size sel atomRadius 0.7

Changed 13 atom radii  

> size sel stickRadius 0.7

Changed 13 bond radii  

> size sel stickRadius 0.5

Changed 13 bond radii  

> size sel stickRadius 0.3

Changed 13 bond radii  

> size sel stickRadius 0.2

Changed 13 bond radii  

> size sel stickRadius 0.25

Changed 13 bond radii  

> size sel stickRadius 0.3

Changed 13 bond radii  

> size sel stickRadius 0.25

Changed 13 bond radii  

> select clear

> save /Users/adastra/Desktop/image354.png supersample 3

> save /Users/adastra/Desktop/CB-Dock2-PFL-poc7-zoom.cxs

——— End of log from Thu Jul 21 18:36:30 2022 ———

opened ChimeraX session  

> ui tool show "Side View"

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> show sel surfaces

> color (#!1 & sel) white

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> show sel surfaces

> color (#!1 & sel) white

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> show sel surfaces

> color (#!1 & sel) white

> ui tool show "Color Actions"

> hide sel surfaces

> select /B:389

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

> select add /B:302

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select add /B:305

27 atoms, 25 bonds, 3 residues, 2 models selected  

> select add /B:306

35 atoms, 32 bonds, 4 residues, 2 models selected  

> select add /B:309

41 atoms, 37 bonds, 5 residues, 2 models selected  

> select add /B:356

49 atoms, 44 bonds, 6 residues, 2 models selected  

> select add /B:357

57 atoms, 51 bonds, 7 residues, 2 models selected  

> select add /C:380

65 atoms, 58 bonds, 8 residues, 2 models selected  

> select add /C:383

70 atoms, 62 bonds, 9 residues, 2 models selected  

> select add /C:384

77 atoms, 68 bonds, 10 residues, 2 models selected  

> select add /B:386

89 atoms, 80 bonds, 11 residues, 2 models selected  

> select ~sel

14404 atoms, 14770 bonds, 8 pseudobonds, 1918 residues, 2 models selected  

> show sel surfaces

> color sel white

> select clear

> undo

> select ~sel

89 atoms, 83 bonds, 11 residues, 1 model selected  

> transparency (#!1 & sel) 40

> select ~sel

14404 atoms, 14770 bonds, 8 pseudobonds, 1918 residues, 2 models selected  

> transparency (#!1 & sel) 50

[Repeated 1 time(s)]

> transparency (#!1 & sel) 0

> select ~sel

89 atoms, 83 bonds, 11 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 50

> select clear

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> transparency (#!1 & sel) 50

> select /C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> transparency (#!1 & sel) 50

> select clear

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel azure

> color sel gray

> color sel dark sea green

> color sel light green

> color sel dark sea green

> color sel lavender

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel linen

> color sel light goldenrod yellow

> color sel pale turquoise

> color sel powder blue

> color sel gainsboro

> color sel light cyan

> color sel gainsboro

> color sel lavender

> color sel light cyan

> color sel light yellow

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light steel blue

> color sel dark sea green

> color sel dark gray

> color sel rosy brown

> color sel burly wood

> color sel tan

> color sel powder blue

> color sel alice blue

> color sel honeydew

> color sel azure

> color sel white smoke

> color sel mint cream

> color sel light sky blue

> transparency (#!1 & sel) 50

> color sel light steel blue

> transparency (#!1 & sel) 50

> select /C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel dim gray

> color sel gray

> color sel dark gray

> color sel light gray

> color sel silver

> color sel light gray

> color sel silver

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel light coral

> color sel pink

> color sel misty rose

> color sel light pink

> color sel misty rose

> select clear

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light gray

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel misty rose

> select clear

> select /C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color (#!1 & sel) white

> transparency (#!1 & sel) 50

> select clear

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel moccasin

> color sel seashell

> color sel lavender blush

> color sel azure

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel moccasin

> color sel pale goldenrod

> color sel lemon chiffon

> color sel light yellow

> select clear

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel light sky blue

> color sel khaki

> color sel pale goldenrod

> color sel light goldenrod yellow

> color sel light yellow

> color sel lemon chiffon

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel light steel blue

> transparency (#!1 & sel) 60

> transparency (#!1 & sel) 40

> transparency (#!1 & sel) 70

> select clear

> select /C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel dark sea green

> transparency (#!1 & sel) 70

> select clear

> select /C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel pale goldenrod

> transparency (#!1 & sel) 70

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel white

> color sel light gray

> color sel silver

> color sel light gray

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel white

> color sel ivory

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting soft

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> select clear

> select up

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

> select up

13 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel red

> color sel #ff7e79ff

> select /B:299@O

1 atom, 1 residue, 1 model selected  

> select /B:302@CB

1 atom, 1 residue, 1 model selected  

> select add /B:306@CD1

2 atoms, 2 residues, 2 models selected  

> select subtract /B:306@CD1

1 atom, 1 residue, 2 models selected  

> select /B:302@CB

1 atom, 1 residue, 1 model selected  

> select /B:302@CG2

1 atom, 1 residue, 1 model selected  

> select /B:302@CD1

1 atom, 1 residue, 1 model selected  

> select /B:302@CB

1 atom, 1 residue, 1 model selected  

> select add /B:306@CD1

2 atoms, 2 residues, 2 models selected  

> select add /B:303@CA

3 atoms, 3 residues, 2 models selected  

> select subtract /B:303@CA

2 atoms, 2 residues, 2 models selected  

> select subtract /B:306@CD1

1 atom, 1 residue, 2 models selected  

> select subtract /B:302@CB

1 model selected  

> select /C:380@CG2

1 atom, 1 residue, 1 model selected  

> select /C:380@CG2

1 atom, 1 residue, 1 model selected  

> select clear

> save /Users/adastra/Desktop/image354.png supersample 3

> save /Users/adastra/Desktop/CB-Dock2-PFL-poc7-zoomout.cxs

> select /A

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> hide sel surfaces

> select /D

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> hide sel surfaces

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> hide sel surfaces

> select /C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> hide sel surfaces

> select clear

> select /B:306

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /B:309

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add /B:356

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select add /B:357

30 atoms, 26 bonds, 4 residues, 2 models selected  

> select add /C:380

38 atoms, 33 bonds, 5 residues, 2 models selected  

> select add /C:383

43 atoms, 37 bonds, 6 residues, 3 models selected  

> select add /C:384

50 atoms, 43 bonds, 7 residues, 3 models selected  

> select add /B:386

62 atoms, 55 bonds, 8 residues, 3 models selected  

> select add /B:305

70 atoms, 62 bonds, 9 residues, 3 models selected  

> select add /B:302

78 atoms, 69 bonds, 10 residues, 3 models selected  

> select add /B:389

89 atoms, 80 bonds, 11 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel light slate gray

> color sel slate gray

> color sel dark sea green

> color sel light steel blue

> color sel pale turquoise

> color sel light blue

> color sel light sky blue

> color sel sky blue

[Repeated 1 time(s)]

> color sel powder blue

> color sel light gray

> color sel silver

> color sel light cyan

> color sel light slate gray

> select /B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel azure

> color sel honeydew

> color sel alice blue

> color sel azure

> select /C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel light yellow

> color sel light goldenrod yellow

> color sel light yellow

> select /B:306

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /B:356

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select add /B:309

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select add /B:305

30 atoms, 26 bonds, 4 residues, 2 models selected  

> select add /B:302

38 atoms, 33 bonds, 5 residues, 2 models selected  

> select add /B:389

49 atoms, 44 bonds, 6 residues, 2 models selected  

> select add /B:386

61 atoms, 56 bonds, 7 residues, 2 models selected  

> select add /C:384

68 atoms, 62 bonds, 8 residues, 2 models selected  

> select add /C:383

73 atoms, 66 bonds, 9 residues, 3 models selected  

> select add /C:380

81 atoms, 73 bonds, 10 residues, 3 models selected  

> select add /B:357

89 atoms, 80 bonds, 11 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel light slate gray

> select clear

> save /Users/adastra/Desktop/CB-Dock2-PFL-poc7-zoom2.cxs

> save /Users/adastra/Desktop/image354.png supersample 3

> select /B:382

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> ui tool show "Color Actions"

> color sel light slate gray

> show sel atoms

> select clear

> save /Users/adastra/Desktop/image354.png supersample 3

[Repeated 1 time(s)]

> save /Users/adastra/Desktop/image355.png supersample 3

> save /Users/adastra/Desktop/CB-Dock2-PFL-poc7-zoom2.cxs

——— End of log from Thu Jul 21 19:12:32 2022 ———

opened ChimeraX session  

> open /Users/adastra/Downloads/5u6o/5u6o.pdb

5u6o.pdb title:  
Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-
gated ion channel [more info...]  
  
Chain information for 5u6o.pdb #2  
---  
Chain | Description | UniProt  
A B C D | potassium/sodium hyperpolarization-activated cyclic nucleotide-gated
channel 1 | HCN1_HUMAN  
  

> open /Users/adastra/5u6p.pdb

5u6p.pdb title:  
Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-
gated ion channel In complex with camp [more info...]  
  
Chain information for 5u6p.pdb #3  
---  
Chain | Description | UniProt  
A B C D | potassium/sodium hyperpolarization-activated cyclic nucleotide-gated
channel 11 | HCN1_HUMAN  
E F G H | brain cyclic nucleotide-gated channel 1 |  
  
Non-standard residues in 5u6p.pdb #3  
---  
CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp)  
  

> open /Users/adastra/7nmn.pdb

7nmn.pdb title:  
Rabbit HCN4 stabilised In amphipol A8-35 [more info...]  
  
Chain information for 7nmn.pdb #4  
---  
Chain | Description | UniProt  
A B C D | potassium/sodium hyperpolarization-activated cyclic nucleotide-gated
channel 4,rabbit HCN4 | HCN4_RABIT  
  

> ui tool show Matchmaker

> matchmaker #!2-4 to #1

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 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
5u6o.pdb, chain A (#2), sequence alignment score = 2205  
RMSD between 472 pruned atom pairs is 0.740 angstroms; (across all 482 pairs:
0.840)  
  
Matchmaker 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
5u6p.pdb, chain A (#3), sequence alignment score = 2162.4  
RMSD between 410 pruned atom pairs is 0.900 angstroms; (across all 482 pairs:
1.550)  
  
Matchmaker 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
7nmn.pdb, chain A (#4), sequence alignment score = 1980.5  
RMSD between 282 pruned atom pairs is 1.101 angstroms; (across all 467 pairs:
5.682)  
  

> matchmaker #!2-4 to #1

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 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
5u6o.pdb, chain A (#2), sequence alignment score = 2205  
RMSD between 472 pruned atom pairs is 0.740 angstroms; (across all 482 pairs:
0.840)  
  
Matchmaker 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
5u6p.pdb, chain A (#3), sequence alignment score = 2162.4  
RMSD between 410 pruned atom pairs is 0.900 angstroms; (across all 482 pairs:
1.550)  
  
Matchmaker 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
7nmn.pdb, chain A (#4), sequence alignment score = 1980.5  
RMSD between 282 pruned atom pairs is 1.101 angstroms; (across all 467 pairs:
5.682)  
  

> select add #1

14493 atoms, 14853 bonds, 8 pseudobonds, 1929 residues, 2 models selected  

> select add #2

28973 atoms, 29693 bonds, 16 pseudobonds, 3857 residues, 8 models selected  

> select add #4

44409 atoms, 45505 bonds, 20 pseudobonds, 5733 residues, 10 models selected  

> select add #3

60049 atoms, 61521 bonds, 28 pseudobonds, 7829 residues, 12 models selected  

> hide sel atoms

> hide sel cartoons

> show sel surfaces

> ui tool show "Side View"

> select add #4

60049 atoms, 61521 bonds, 28 pseudobonds, 7829 residues, 35 models selected  

> select add #3

60049 atoms, 61521 bonds, 28 pseudobonds, 7829 residues, 45 models selected  

> select add #2

60049 atoms, 61521 bonds, 28 pseudobonds, 7829 residues, 53 models selected  

> select add #1

60049 atoms, 61521 bonds, 28 pseudobonds, 7829 residues, 60 models selected  

> select subtract #4

44613 atoms, 45709 bonds, 24 pseudobonds, 5953 residues, 51 models selected  

> select subtract #3

28973 atoms, 29693 bonds, 16 pseudobonds, 3857 residues, 35 models selected  

> select subtract #2

14493 atoms, 14853 bonds, 8 pseudobonds, 1929 residues, 17 models selected  

> select subtract #1

4 models selected  

> hide #!2 models

> hide #!4 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> open /Users/adastra/Downloads/6uqf.pdb

6uqf.pdb title:  
Human HCN1 channel In A hyperpolarized conformation [more info...]  
  
Chain information for 6uqf.pdb #5  
---  
Chain | Description | UniProt  
A B C D | potassium/sodium hyperpolarization-activated cyclic nucleotide-gated
channel 1 | HCN1_HUMAN  
  
Non-standard residues in 6uqf.pdb #5  
---  
CMP — adenosine-3',5'-cyclic-monophosphate (cyclic amp; camp)  
HG — mercury (II) ion  
  

> ui tool show Matchmaker

> matchmaker #!5 to #1

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 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
6uqf.pdb, chain A (#5), sequence alignment score = 2104.7  
RMSD between 292 pruned atom pairs is 1.125 angstroms; (across all 480 pairs:
3.838)  
  

> matchmaker #!5 to #1

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 21jul08_HCN1_PFL_out_7.-6.3.complex.pdb, chain A (#1) with
6uqf.pdb, chain A (#5), sequence alignment score = 2104.7  
RMSD between 292 pruned atom pairs is 1.125 angstroms; (across all 480 pairs:
3.838)  
  

> select add #5

16528 atoms, 16904 bonds, 4 pseudobonds, 2132 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> show sel surfaces

> hide #!5 models

> select subtract #5

4 models selected  

> color #!4 bychain

> show #!1 models

> show #!2 models

> show #!3 models

> show #!5 models

> select add #5

16528 atoms, 16904 bonds, 4 pseudobonds, 2132 residues, 9 models selected  

> select add #4

31964 atoms, 32716 bonds, 8 pseudobonds, 4008 residues, 22 models selected  

> select add #2

46444 atoms, 47556 bonds, 16 pseudobonds, 5936 residues, 35 models selected  

> select add #1

60937 atoms, 62409 bonds, 24 pseudobonds, 7865 residues, 48 models selected  

> hide #!2 models

> hide #!4 models

> hide #!3 models

> hide #!5 models

> select subtract #5

44409 atoms, 45505 bonds, 20 pseudobonds, 5733 residues, 29 models selected  

> select subtract #4

28973 atoms, 29693 bonds, 16 pseudobonds, 3857 residues, 23 models selected  

> select subtract #2

14493 atoms, 14853 bonds, 8 pseudobonds, 1929 residues, 17 models selected  

> select subtract #1

4 models selected  

> select add #1

14493 atoms, 14853 bonds, 8 pseudobonds, 1929 residues, 9 models selected  

> select #1/PFL

Nothing selected  

> show #!1 atoms

> style #1 sphere

Changed 14493 atom styles  

> style #!1 ball

Changed 14493 atom styles  

> style #!1 sphere

Changed 14493 atom styles  

> style #!1 stick

Changed 14493 atom styles  

> style #!1 ball

Changed 14493 atom styles  

> color #1 red

> select #1/C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel pale goldenrod

> color sel light goldenrod yellow

> select #1/B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> select down

3620 atoms, 3712 bonds, 2 pseudobonds, 482 residues, 3 models selected  

> select down

3620 atoms, 3712 bonds, 2 pseudobonds, 482 residues, 3 models selected  

> select down

3620 atoms, 3712 bonds, 2 pseudobonds, 482 residues, 3 models selected  

> select down

3620 atoms, 3712 bonds, 2 pseudobonds, 482 residues, 3 models selected  

> select down

3620 atoms, 3712 bonds, 2 pseudobonds, 482 residues, 3 models selected  

> select down

3620 atoms, 3712 bonds, 2 pseudobonds, 482 residues, 3 models selected  

> select add #1/?:1@@serial_number=14

3621 atoms, 3714 bonds, 2 pseudobonds, 483 residues, 3 models selected  

> select add #1/?:1@@serial_number=13

3622 atoms, 3714 bonds, 2 pseudobonds, 483 residues, 3 models selected  

> select add #1/?:1@@serial_number=6

3623 atoms, 3718 bonds, 2 pseudobonds, 483 residues, 3 models selected  

> select add #1/?:1@@serial_number=9

3624 atoms, 3722 bonds, 2 pseudobonds, 483 residues, 3 models selected  

> color sel alice blue

> color sel light steel blue

> select clear

> select #1/A,D

7240 atoms, 7420 bonds, 4 pseudobonds, 964 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

[Repeated 1 time(s)]

> hide sel atoms

> show sel surfaces

> color (#!1 & sel) white

> select clear

> select up

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

> select up

13 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel red

> show sel surfaces

> show sel atoms

[Repeated 1 time(s)]

> style (#!1 & sel) sphere

Changed 13 atom styles  

> color sel red

> select clear

> select #1/?:1@@serial_number=13

1 atom, 1 residue, 1 model selected  

> select up

13 atoms, 13 bonds, 1 residue, 2 models selected  

> hide sel surfaces

> style (#!1 & sel) ball

Changed 13 atom styles  

> surface style #1.6 dot

> show sel surfaces

> select clear

> select #1/?:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select up

13 atoms, 13 bonds, 1 residue, 2 models selected  

> surface style #1.6 solid

> select clear

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> select #2/C:380@CG2

1 atom, 1 residue, 1 model selected  

> select #2/C

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel light goldenrod yellow

> select #2/B

3620 atoms, 3710 bonds, 2 pseudobonds, 482 residues, 2 models selected  

> color sel light steel blue

> select #2/A,D

7240 atoms, 7420 bonds, 4 pseudobonds, 964 residues, 2 models selected  

> color sel white

> select clear

> show #!4 models

> hide #!2 models

> select #4/A,D

7718 atoms, 7906 bonds, 2 pseudobonds, 938 residues, 2 models selected  

> color sel white

> select #4/B

3859 atoms, 3953 bonds, 1 pseudobond, 469 residues, 2 models selected  

> color sel light goldenrod yellow

> color sel light steel blue

> select #4/C

3859 atoms, 3953 bonds, 1 pseudobond, 469 residues, 2 models selected  

> color sel light goldenrod yellow

> select clear

> show #!5 models

> hide #!4 models

> select #5/C

4132 atoms, 4226 bonds, 1 pseudobond, 533 residues, 2 models selected  

> color sel light goldenrod yellow

> select #5/B

4132 atoms, 4226 bonds, 1 pseudobond, 533 residues, 2 models selected  

> color sel light steel blue

> select #5/A,D

8264 atoms, 8452 bonds, 2 pseudobonds, 1066 residues, 2 models selected  

> color sel white

> select clear

> show #!4 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!1 models

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> view

> lighting soft

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!4 models

> hide #!5 models

> hide #!4 models

> show #!2 models

> show #!1 models

> hide #!2 models

> select #1/?:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select up

13 atoms, 13 bonds, 1 residue, 2 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> show sel atoms

> show sel surfaces

> hide sel surfaces

> select clear

> select up

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

> select up

13 atoms, 13 bonds, 1 residue, 2 models selected  

> show sel surfaces

> select clear

> save "/Users/adastra/Desktop/pocket with pfl.png" width 3000 height 2436
> supersample 4 transparentBackground true

> hide #!1 models

> show #!2 models

> save "/Users/adastra/Desktop/pocket 5u6o.png" width 3000 height 2436
> supersample 4

> hide #!2 models

> show #!4 models

> save "/Users/adastra/Desktop/pocket 7nmn.png" width 3000 height 2436
> supersample 4 transparentBackground true

> show #!5 models

> hide #!4 models

> save "/Users/adastra/Desktop/pocket 6uqf.png" width 3000 height 2436
> supersample 4 transparentBackground true

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!5 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/sideview/tool.py", line 113, in _redraw  
self.render()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/sideview/tool.py", line 288, in render  
self.view.draw()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 177, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 227, in _draw_scene  
camera.draw_background(vnum, r)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/camera.py", line 184, in draw_background  
render.draw_background()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1178, 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.  
  




OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 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: 32 GB
      System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5058.0.0,0)
      OS Loader Version: 577~170

Software:

    System Software Overview:

      System Version: macOS 13.4 (22F66)
      Kernel Version: Darwin 22.5.0
      Time since boot: 5 days, 10 hours, 13 minutes

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 Support: Metal 3

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL S2340M:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 293M34CA00PT
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Analog VGA or Analog Over DVI-I
          Adapter Firmware Version:  1.0d


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Tom Goddard]

Graphics error after a long session of commands. On a dual GPU (Intel + Radeon) Mac laptop with two displays. I suspect it is a Mac OpenGL issue with that configuration.