glClear: invalid framebuffer operation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | Data format provider 'LAMMPS coordinates' supplied unknown keywords
with format description: {'default_for': '.data'}  
Data format provider 'LAMMPS trajectory' supplied unknown keywords with format
description: {'default_for': '.dump'}  
Data format provider 'LAMMPS coordinates' supplied unknown keywords with
format description: {'default_for': '.data'}  
Data format provider 'LAMMPS trajectory' supplied unknown keywords with format
description: {'default_for': '.dump'}  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/zchen/Desktop/ESX_project/7_AF2/EccC4/1.pdb

Chain information for 1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/zchen/Desktop/ESX_project/7_AF2/EccC4/2.pdb

Chain information for 2.pdb  
---  
Chain | Description  
2.1/A 2.2/A | No description available  
  

> open /Users/zchen/Desktop/ESX_project/7_AF2/EccC4/3.pdb

Chain information for 3.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> hide #!2 models

> select add #1

10005 atoms, 10214 bonds, 1311 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2.1/A #2.2/A #3/A

Alignment identifier is 1  

> select #1/A:449 #2.1/A:449 #2.2/A:449 #3/A:449

16 atoms, 12 bonds, 4 residues, 4 models selected  

> select #1/A:449-572 #2.1/A:449-572 #2.2/A:449-572 #3/A:449-572

3648 atoms, 3688 bonds, 496 residues, 4 models selected  
1 [ID: 1] region 4 chains [449-572] RMSD: 0.000  
  

> select #1/A:648-649 #2.1/A:648-649 #2.2/A:648-649 #3/A:648-649

68 atoms, 64 bonds, 8 residues, 4 models selected  

> select #1/A:449-649 #2.1/A:449-649 #2.2/A:449-649 #3/A:449-649

6100 atoms, 6192 bonds, 804 residues, 4 models selected  
1 [ID: 1] region 4 chains [449-649] RMSD: 0.000  
  

> color (#1 & sel) blue

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select ~sel

33920 atoms, 34656 bonds, 4440 residues, 5 models selected  

> select clear

> undo

> ui tool show "Segment Map"

> delete atoms (#1 & sel)

> delete bonds (#1 & sel)

> hide #1 models

> show #!2 models

> select add #2

28490 atoms, 29092 bonds, 3732 residues, 4 models selected  

> select add #3

30015 atoms, 30642 bonds, 3933 residues, 4 models selected  

> select subtract #2

10005 atoms, 10214 bonds, 1311 residues, 1 model selected  

> select add #2

30015 atoms, 30642 bonds, 3933 residues, 4 models selected  

> select subtract #2

10005 atoms, 10214 bonds, 1311 residues, 1 model selected  

> select #1/A:518-563 #2.1/A:518-563 #2.2/A:518-563 #3/A:518-563

1404 atoms, 1408 bonds, 184 residues, 4 models selected  

> select #1/A:518-649 #2.1/A:518-700 #2.2/A:518-700 #3/A:518-700

5279 atoms, 5378 bonds, 681 residues, 4 models selected  
1 [ID: 1] region 4 chains [518-700] RMSD: 0.000  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2.1/A #2.2/A #3/A

Alignment identifier is 1  

> select #2.1/A:802-803 #2.2/A:802-803 #3/A:802-803

57 atoms, 54 bonds, 6 residues, 3 models selected  

> select #2.1/A:802-1121 #2.2/A:802-1121 #3/A:802-1121

7347 atoms, 7485 bonds, 960 residues, 3 models selected  
1 [ID: 1] region 4 chains [802-1121] RMSD: 0.000  
  

> select #2.1/A:995 #2.2/A:995 #3/A:995

24 atoms, 21 bonds, 3 residues, 3 models selected  

> select #2.1/A:808-995 #2.2/A:808-995 #3/A:808-995

4272 atoms, 4350 bonds, 564 residues, 3 models selected  
1 [ID: 1] region 4 chains [808-995] RMSD: 0.000  
  

> select #2.1/A:1-448,650-1311 #2.2/A:1-448,650-1311 #3/A:1-448,650-1311

25440 atoms, 25992 bonds, 3330 residues, 3 models selected  

> select #2.1/A:802 #2.2/A:802 #3/A:802

33 atoms, 30 bonds, 3 residues, 3 models selected  

> select #2.1/A:802-995 #2.2/A:802-995 #3/A:802-995

4431 atoms, 4515 bonds, 582 residues, 3 models selected  
1 [ID: 1] region 4 chains [802-995] RMSD: 0.000  
  

> select ~sel

27109 atoms, 27669 bonds, 3552 residues, 5 models selected  

> delete atoms (#2.1-2 & sel)

> delete bonds (#2.1-2 & sel)

> hide #!2 models

> show #1 models

> hide #1 models

> show #!2 models

> show #3 models

> hide #!2 models

> select add #2

13007 atoms, 13265 bonds, 1706 residues, 5 models selected  

> select add #3

14484 atoms, 14772 bonds, 1900 residues, 5 models selected  

> select subtract #2

11530 atoms, 11762 bonds, 1512 residues, 2 models selected  

> select subtract #1

10005 atoms, 10214 bonds, 1311 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2.1/A #2.2/A #3/A

Alignment identifier is 1  

> select #3/A:1093

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

> select #3/A:1093-1275

1431 atoms, 1459 bonds, 183 residues, 1 model selected  

> select #3/A:1273

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

> select #3/A:1093-1273

1418 atoms, 1446 bonds, 181 residues, 1 model selected  

> select ~sel

13066 atoms, 13324 bonds, 1719 residues, 5 models selected  

> delete atoms (#3 & sel)

> delete bonds (#3 & sel)

> select subtract #2

1525 atoms, 1548 bonds, 201 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #1 models

> show #!2 models

> ui tool show "Modeller Comparative"

> select add #1

1525 atoms, 1548 bonds, 201 residues, 1 model selected  

> select add #2

4479 atoms, 4558 bonds, 589 residues, 4 models selected  

> select add #3

5897 atoms, 6004 bonds, 770 residues, 5 models selected  

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> save /Users/zchen/Desktop/1.pdb models #1 relModel #1

> select subtract #1

4372 atoms, 4456 bonds, 569 residues, 4 models selected  

> select subtract #2

1418 atoms, 1446 bonds, 181 residues, 1 model selected  

> select subtract #3

Nothing selected  

> ui tool show "Color Actions"

> color byelement

> color bychain

[Repeated 1 time(s)]

> color byelement

> color #1 #ff40ffff

> color #2 #942192ff models

> ui tool show Matchmaker

> matchmaker #3#2.1 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 1.pdb, chain A (#1) with 3.pdb, chain A (#3), sequence alignment
score = 232.7  
RMSD between 90 pruned atom pairs is 0.898 angstroms; (across all 171 pairs:
5.171)  
  
Matchmaker 1.pdb, chain A (#1) with 2.pdb, chain A (#2.1), sequence alignment
score = 360.1  
RMSD between 116 pruned atom pairs is 1.125 angstroms; (across all 190 pairs:
2.996)  
  

> close #2.2

> select add #2

1477 atoms, 1505 bonds, 194 residues, 2 models selected  

> hide #3 models

> hide #2.1 models

> hide #!2 models

> hide #1 models

> show #1 models

> show #2.1 models

> color #2.1 #00f900ff

> show #3 models

> open /Users/zchen/Desktop/ESX_project/7_AF2/EccC4/ranked_0.pdb

Chain information for ranked_0.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> hide #2.1 models

> hide #!2 models

> hide #1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2.1/A #3/A #4/A

Alignment identifier is 1  

> select #1/A:476 #4/A:476

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:476-478 #4/A:476-478

38 atoms, 36 bonds, 6 residues, 2 models selected  
1 [ID: 1] region 4 chains [476-478] RMSD: 0.000  
  

> select #4/A:438

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A #4/A:438-709

3571 atoms, 3632 bonds, 473 residues, 2 models selected  
1 [ID: 1] region 4 chains [438-709] RMSD: 0.000  
  

> select #4/A:697

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A #4/A:438-697

3500 atoms, 3560 bonds, 461 residues, 2 models selected  
1 [ID: 1] region 4 chains [438-697] RMSD: 0.000  
  

> color (#4 & sel) red

> select #4/A:400-401

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

> select #4/A:400-403

33 atoms, 32 bonds, 4 residues, 1 model selected  

> select #4/A:400-401

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

> select #1/A #4/A:400-660

3516 atoms, 3572 bonds, 462 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-660] RMSD: 0.000  
  

> select #4/A:697

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A #4/A:400-697

3803 atoms, 3869 bonds, 499 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-697] RMSD: 0.000  
  

> color (#4 & sel) blue

> select #4/A:1311

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #4/A:1311

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #4/A:400

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

> select #1/A #4/A:400-761

4264 atoms, 4341 bonds, 563 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-761] RMSD: 0.000  
  

> color (#4 & sel) red

> select #4/A:410

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:449-597 #4/A:410-597

2530 atoms, 2571 bonds, 337 residues, 2 models selected  
1 [ID: 1] region 4 chains [410-597] RMSD: 0.000  
  

> select #4/A:400

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

> select #1/A:449-563 #4/A:400-563

2077 atoms, 2102 bonds, 279 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-563] RMSD: 0.000  
  

> select #1/A #2.1/A #3/A #4/A

14425 atoms, 14713 bonds, 1887 residues, 4 models selected  

> select #4/A:730

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

> select #1/A #4/A:400-730

4030 atoms, 4101 bonds, 532 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-730] RMSD: 0.000  
  

> color (#4 & sel) orange red

> color (#4 & sel) blue

> select #4/A:438

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A #4/A:438-709

3571 atoms, 3632 bonds, 473 residues, 2 models selected  
1 [ID: 1] region 4 chains [438-709] RMSD: 0.000  
  

> select #4/A:697-698

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #1/A:483-649 #4/A:483-698

2951 atoms, 3002 bonds, 383 residues, 2 models selected  
1 [ID: 1] region 4 chains [483-698] RMSD: 0.000  
  

> color (#4 & sel) purple

> select #4/A:760

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

> select #2.1/A #4/A:760-1030

3553 atoms, 3623 bonds, 465 residues, 2 models selected  
1 [ID: 1] region 4 chains [760-1030] RMSD: 51.532  
  

> select #4/A:1060

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

> select #2.1/A #4/A:760-1060

3769 atoms, 3840 bonds, 495 residues, 2 models selected  
1 [ID: 1] region 4 chains [760-1060] RMSD: 51.532  
  

> color (#4 & sel) magenta

> select #4/A:1061

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

> select #3/A #4/A:1061-1311

3371 atoms, 3440 bonds, 432 residues, 2 models selected  
1 [ID: 1] region 4 chains [1061-1311] RMSD: 97.042  
  

> color (#4 & sel) hot pink

> color (#4 & sel) lime

> select #4/A:354-399

339 atoms, 344 bonds, 46 residues, 1 model selected  

> select #4/A:354-443

694 atoms, 706 bonds, 90 residues, 1 model selected  

> select #4/A:399-400

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #1/A #4/A:399-712

3901 atoms, 3969 bonds, 515 residues, 2 models selected  
1 [ID: 1] region 4 chains [399-712] RMSD: 0.000  
  

> select #4/A:759

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A #4/A:399-759

4253 atoms, 4329 bonds, 562 residues, 2 models selected  
1 [ID: 1] region 4 chains [399-759] RMSD: 0.000  
  

> select #4/A:400-445

367 atoms, 373 bonds, 46 residues, 1 model selected  

> select #1/A #4/A:400-760

4257 atoms, 4333 bonds, 562 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-760] RMSD: 0.000  
  

> color (#4 & sel) red

> open /Users/zchen/Desktop/ESX_project/7_AF2/EccC4/ranked_1.pdb

Chain information for ranked_1.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #4 models

> select add #4

11530 atoms, 11762 bonds, 1512 residues, 2 models selected  

> select #4/A:400

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

> select #1/A #4/A:400-754

4204 atoms, 4277 bonds, 556 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-754] RMSD: 0.000  
  

> select #4/A:759

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A #4/A:400-759

4249 atoms, 4325 bonds, 561 residues, 2 models selected  
1 [ID: 1] region 4 chains [400-759] RMSD: 0.000  
  

> color #5 orange red

> select add #4

11530 atoms, 11762 bonds, 1512 residues, 2 models selected  

> select subtract #4

1525 atoms, 1548 bonds, 201 residues, 1 model selected  

> select add #5

11530 atoms, 11762 bonds, 1512 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2.1/A #3/A #4/A #5/A

Alignment identifier is 1  

> select #4/A:400 #5/A:400

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

> select #1/A #2.1/A:802-804 #4/A:400-804 #5/A:400-804

7687 atoms, 7836 bonds, 1014 residues, 4 models selected  
1 [ID: 1] region 5 chains [400-804] RMSD: 25.165  
  

> select #4/A:400 #5/A:400

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

> select #1/A #4/A:400-714 #5/A:400-714

6293 atoms, 6408 bonds, 831 residues, 3 models selected  
1 [ID: 1] region 5 chains [400-714] RMSD: 22.212  
  

> select #4/A:759 #5/A:759

28 atoms, 30 bonds, 2 residues, 2 models selected  

> select #1/A #4/A:400-759 #5/A:400-759

6973 atoms, 7102 bonds, 921 residues, 3 models selected  
1 [ID: 1] region 5 chains [400-759] RMSD: 25.139  
  

> color (#5 & sel) blue

> select #4/A:760 #5/A:760

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

> select #2.1/A #4/A:760-1062 #5/A:760-1062

6091 atoms, 6207 bonds, 800 residues, 3 models selected  
1 [ID: 1] region 5 chains [760-1062] RMSD: 43.704  
  

> color (#5 & sel) cyan

> open
> /Users/zchen/Desktop/ESX4_modeling/ESX4-latest_EM_map/ESX4-CR/cryosparc_P109_J3619_004_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P109_J3619_004_volume_map_sharp.mrc as #6, grid size
380,380,380, pixel 0.89, shown at level 0.051, step 2, values float32  

> open
> /Users/zchen/Desktop/ESX4_modeling/ESX4-latest_EM_map/ESX4-CR/cryosparc_P109_J3619_004_volume_map.mrc
> format mrc

Opened cryosparc_P109_J3619_004_volume_map.mrc as #7, grid size 380,380,380,
pixel 0.89, shown at level 0.0475, step 2, values float32  

> open
> /Users/zchen/Desktop/ESX4_modeling/ESX4-latest_EM_map/ESX4-Glob/cryosparc_P109_J3591_006_volume_map.mrc

Opened cryosparc_P109_J3591_006_volume_map.mrc as #8, grid size 380,380,380,
pixel 0.89, shown at level 0.0626, step 2, values float32  

> lighting full

> volume #8 step 1

> volume #8 level 0.07446

> volume #8 level 0.02609

> volume #8 level 0.05214

> volume #8 level 0.03279

> volume #8 level 0.01791

> volume #8 level 0.01419

> open
> /Users/zchen/Desktop/ESX_project/7_AF2/AF3/fold_ecce4/fold_ecce4_model_0.cif

Chain information for fold_ecce4_model_0.cif #9  
---  
Chain | Description  
A | .  
  

> hide #!8 models

> select add #9

10220 atoms, 10421 bonds, 1344 residues, 4 models selected  

> hide #5 models

> hide #9 models

> show #4 models

> ui mousemode right zoom

> select #1/A #2.1/A #3/A #4/A #5/A

24430 atoms, 24927 bonds, 3198 residues, 5 models selected  

> show sel & #4 cartoons

[Repeated 1 time(s)]

> hide sel & #4 cartoons

[Repeated 1 time(s)]

> show sel & #4 cartoons

> show sel & #4 atoms

> color (#4 & sel) byelement

> hide #4 models

> show #4 models

> select subtract #4

14425 atoms, 14713 bonds, 1887 residues, 4 models selected  

> select #3/A:1165 #4/A:1165 #5/A:1165

21 atoms, 18 bonds, 3 residues, 3 models selected  

> select #3/A:1165 #4/A:1165 #5/A:1165

21 atoms, 18 bonds, 3 residues, 3 models selected  
1 [ID: 1] region 5 chains [1165] RMSD: 80.165  
  

> select #1/A #2.1/A #3/A #4/A #5/A

24430 atoms, 24927 bonds, 3198 residues, 5 models selected  

> select #4/A:1066-1067 #5/A:1066-1067

40 atoms, 40 bonds, 4 residues, 2 models selected  

> select #3/A #4/A:1066-1311 #5/A:1066-1311

5240 atoms, 5346 bonds, 673 residues, 3 models selected  
1 [ID: 1] region 5 chains [1066-1311] RMSD: 80.882  
  

> select #4/A:1066 #5/A:1066

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

> select #4/A:1066-1074 #5/A:1066-1074

132 atoms, 134 bonds, 18 residues, 2 models selected  
1 [ID: 1] region 5 chains [1066-1074] RMSD: 22.673  
  

> select #1/A #2.1/A #3/A #4/A #5/A

24430 atoms, 24927 bonds, 3198 residues, 5 models selected  

> select #3/A:1207 #4/A:1207 #5/A:1207

24 atoms, 21 bonds, 3 residues, 3 models selected  

> select #3/A:1207-1213 #4/A:1207-1213 #5/A:1207-1213

168 atoms, 168 bonds, 21 residues, 3 models selected  
1 [ID: 1] region 5 chains [1207-1213] RMSD: 78.105  
  

> select #3/A:1093 #4/A:1093 #5/A:1093

24 atoms, 21 bonds, 3 residues, 3 models selected  

> select #3/A #4/A:1093-1311 #5/A:1093-1311

4824 atoms, 4922 bonds, 619 residues, 3 models selected  
1 [ID: 1] region 5 chains [1093-1311] RMSD: 82.483  
  

> select #3/A:1093 #4/A:1093 #5/A:1093

24 atoms, 21 bonds, 3 residues, 3 models selected  

> select #3/A:1093-1109 #4/A:1093-1109 #5/A:1093-1109

420 atoms, 435 bonds, 51 residues, 3 models selected  
1 [ID: 1] region 5 chains [1093-1109] RMSD: 83.612  
  

> color (#4 & sel) magenta

> ui mousemode right select

> select clear

> select #3/A:1093 #4/A:1092-1093 #5/A:1092-1093

42 atoms, 39 bonds, 5 residues, 3 models selected  

> select #3/A:1093 #4/A:1064-1093 #5/A:1064-1093

474 atoms, 479 bonds, 61 residues, 3 models selected  
1 [ID: 1] region 5 chains [1064-1093] RMSD: 37.254  
  

> select #1/A #2.1/A #3/A #4/A #5/A

24430 atoms, 24927 bonds, 3198 residues, 5 models selected  

> select #4/A:1057-1058 #5/A:1057-1058

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

> select #4/A:1057-1060 #5/A:1057-1060

70 atoms, 68 bonds, 8 residues, 2 models selected  
1 [ID: 1] region 5 chains [1057-1060] RMSD: 11.180  
  

> select clear

[Repeated 1 time(s)]Drag select of 25 atoms, 9 residues, 17 bonds  

> select clear

> ui mousemode right "translate selected models"

> ui mousemode right zoom

> hide #4 atoms

> select #1/A #2.1/A #3/A #4/A #5/A

24430 atoms, 24927 bonds, 3198 residues, 5 models selected  

> select #4/A:1060-1061 #5/A:1060-1061

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

> select #3/A #4/A:1060-1311 #5/A:1060-1311

5340 atoms, 5450 bonds, 685 residues, 3 models selected  
1 [ID: 1] region 5 chains [1060-1311] RMSD: 80.491  
  

> color (#4 & sel) orange red

> select #1/A:611-649 #4/A:611-656 #5/A:611-656

1039 atoms, 1053 bonds, 131 residues, 3 models selected  

> select #1/A:611-649 #2.1/A:802-926 #4/A:611-926 #5/A:611-926

6031 atoms, 6157 bonds, 796 residues, 4 models selected  
1 [ID: 1] region 5 chains [611-926] RMSD: 42.696  
  

> select #1/A #2.1/A #3/A #4/A #5/A

24430 atoms, 24927 bonds, 3198 residues, 5 models selected  

> select #4/A:400-401 #5/A:400-401

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

> select #1/A #4/A:400-795 #5/A:400-795

7491 atoms, 7634 bonds, 993 residues, 3 models selected  
1 [ID: 1] region 5 chains [400-795] RMSD: 24.942  
  

> select #4/A:772-774 #5/A:772-774

46 atoms, 46 bonds, 6 residues, 2 models selected  

> select #1/A #4/A:400-772 #5/A:400-772

7161 atoms, 7296 bonds, 947 residues, 3 models selected  
1 [ID: 1] region 5 chains [400-772] RMSD: 24.971  
  

> color (#4 & sel) cyan

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.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,)  
)  
  
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-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.6.1.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,)  
)  
  
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.  
  
GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glBlitFramebuffer,  
cArguments = (  
0,  
0,  
1384,  
965,  
0,  
0,  
1384,  
965,  
GL_COLOR_BUFFER_BIT,  
GL_NEAREST,  
)  
)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Applications/ChimeraX-1.6.1.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-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 266, in _draw_scene  
offscreen.finish(r)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1745, in finish  
cfb.copy_from_framebuffer(fb, depth=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2285, in copy_from_framebuffer  
GL.glBlitFramebuffer(0, 0, w, h, 0, 0, w, h, what, GL.GL_NEAREST)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glBlitFramebuffer,  
cArguments = (  
0,  
0,  
1384,  
965,  
0,  
0,  
1384,  
965,  
GL_COLOR_BUFFER_BIT,  
GL_NEAREST,  
)  
)  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: Z12B000LSD/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 13 days, 7 hours, 37 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P2720D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2720D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    biopython: 1.83
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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-ISOLDE: 1.6.0
    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: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    DiffFit: 0.6.2
    docutils: 0.19
    et-xmlfile: 1.1.0
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    fsspec: 2024.10.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openpyxl: 3.1.3
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.2.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    seaborn: 0.13.2
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    sympy: 1.13.3
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    torch: 2.2.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.12.2
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Tom Goddard]

Error in glClear() trying to draw the status line after an expose event. Then subsequent errors trying to draw graphics in glBlitFramebuffer(). User has 3 displays. I suspect the status line drawing failure is related to that.