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Opened 5 months ago
Closed 5 months ago
#18082 closed defect (can't reproduce)
glClear: invalid framebuffer operation
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/zchen/Desktop/ESX-4-model_2.cxs
Log from Tue Jun 24 16:09:32 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/zchen/Desktop/EccE4-ESX-4-colored-model.cxs
Log from Wed Jun 4 15:29:38 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/zchen/Desktop/ESX4_model/Model_update/2nd_model_with_EccE4/job249_refined_modified.cif
Summary of feedback from opening
/Users/zchen/Desktop/ESX4_model/Model_update/2nd_model_with_EccE4/job249_refined_modified.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 37
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for job249_refined_modified.cif #1
---
Chain | Description
B1 | No description available
B2 | No description available
C1 | No description available
C2 | No description available
D1 | No description available
D2 | No description available
D3 | No description available
D4 | No description available
E1 E2 | No description available
P | No description available
> set bgColor white
> show atoms
> show cartoons
Computing secondary structure
> hide atoms
> 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 /B1
3645 atoms, 3719 bonds, 492 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange
> select /B2
3508 atoms, 3579 bonds, 472 residues, 1 model selected
> color sel orange
> select /C1
9744 atoms, 9944 bonds, 1 pseudobond, 1271 residues, 2 models selected
> color sel cyan
> select /C2
9737 atoms, 9937 bonds, 1 pseudobond, 1270 residues, 2 models selected
> color sel cyan
> select /D1
3314 atoms, 3376 bonds, 2 pseudobonds, 464 residues, 2 models selected
> color sel lime green
> select /D2
3116 atoms, 3176 bonds, 2 pseudobonds, 435 residues, 2 models selected
> color sel lime green
> select /D3
3137 atoms, 3195 bonds, 1 pseudobond, 437 residues, 2 models selected
> color sel forest green
> select /D4
3153 atoms, 3211 bonds, 1 pseudobond, 439 residues, 2 models selected
> color sel forest green
> select /E1
4062 atoms, 4146 bonds, 534 residues, 1 model selected
> color sel dark orchid
> color sel medium orchid
[Repeated 2 time(s)]
> select /E2
4062 atoms, 4146 bonds, 534 residues, 1 model selected
> color sel medium orchid
> select /P
3172 atoms, 3249 bonds, 434 residues, 1 model selected
> color sel red
> select add #1
50650 atoms, 51678 bonds, 8 pseudobonds, 6782 residues, 2 models selected
> select subtract #1
Nothing selected
> save /Users/zchen/Desktop/EccE4-ESX-4-colored-model.cxs includeMaps true
——— End of log from Wed Jun 4 15:29:38 2025 ———
opened ChimeraX session
> lighting soft
[Repeated 1 time(s)]
> 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
> cartoon style width 2.0 thickness 0.2
> cartoon style width 1.0 thickness 0.2
> cartoon style width 1.0 thickness 0.5
> cartoon style width 1.0 thickness 0.7
> cartoon style width 1.5 thickness 0.7
> cartoon style width 1.5 thickness 0.5
> cartoon style helix width 2 thickness 0.2
> cartoon style helix width 1 thickness 0.2
> cartoon style helix width 1.2 thickness 0.2
> cartoon style helix width 1.2 thickness 0.5
> cartoon style strand xsection rectangle width 1.2
> cartoon style strand xsection rectangle width 1.5
> cartoon style helix width 1.2 thickness 1
> cartoon style helix width 1.2 thickness 0.5
> save /Users/zchen/Desktop Esx4_cartoon_1.png supersample 8
> transparentBackground true width 2400 height 2400
Cannot determine format for '/Users/zchen/Desktop'
> save /Users/zchen/Desktop Esx4_cartoon_1.png supersample 8
> transparentBackground true width 2400 height 2400
Cannot determine format for '/Users/zchen/Desktop'
> save /Users/zchen/Desktop/ Esx4_cartoon_1.png supersample 8
> transparentBackground true width 2400 height 2400
Cannot determine format for '/Users/zchen/Desktop/'
> save Esx4_cartoon_1.png supersample 8 transparentBackground true width 2400
> height 2400
> cartoon style width 1.5 thickness 1
> save Esx4_cartoon_2.png supersample 8 transparentBackground true width 2400
> height 2400
> save /Users/zchen/Desktop/x4-model-new-style.cxs includeMaps true
> ui tool show "Show Sequence Viewer"
> sequence chain /B1
Alignment identifier is 1/B1
> ui tool show "Show Sequence Viewer"
> sequence chain /B2
Alignment identifier is 1/B2
> select /B2:410
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B2:410
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> ui tool show "Color Actions"
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain /P
Alignment identifier is 1/P
> select /P:85-86
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /P:85-86
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /P:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:85-86
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /P:85-86
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /P:84-85
20 atoms, 19 bonds, 2 residues, 1 model selected
> select /P:84-85
20 atoms, 19 bonds, 2 residues, 1 model selected
> select /P:85
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /B2:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B2:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select /P:389
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /P:389
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 10 atom styles
> ui tool show "Side View"
> select /P:390
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /P:390
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /P:390
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /P:388-389
15 atoms, 15 bonds, 2 residues, 1 model selected
> select /P:388
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /P:388
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /P:388
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /P:388
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /P:433
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:433
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:433
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:433
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:432
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:432
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:433
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:433
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /P:433
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B2:410@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /P:85@NH1
9 atoms, 7 bonds, 2 residues, 1 model selected
> select up
19 atoms, 17 bonds, 2 residues, 1 model selected
> view sel
> select add /B2:415@OE2
20 atoms, 17 bonds, 3 residues, 1 model selected
> select up
28 atoms, 25 bonds, 3 residues, 1 model selected
> select add /P:389@NE2
29 atoms, 25 bonds, 4 residues, 1 model selected
> select up
38 atoms, 35 bonds, 4 residues, 1 model selected
> view sel
[Repeated 1 time(s)]
> select clear
> transparency #1/B2, P 40 target c
> transparency #1/B2, P 30 target c
> hbonds reveal true
5861 hydrogen bonds found
> undo
> hide hb
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> undo
[Repeated 1 time(s)]
> hide sel atoms
> show sel atoms
> ~hbonds
> select up
434 atoms, 443 bonds, 57 residues, 1 model selected
> select down
38 atoms, 35 bonds, 4 residues, 1 model selected
> transparency #1/B2, P 30 target c
> hide sel cartoons
> show sel cartoons
> select clear
> hide atoms
> select #1/B2:410, P:85
20 atoms, 19 bonds, 2 residues, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> select #1/P:85
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/P:389
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B2:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select /P:85@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /B2:410@OD1
12 atoms, 10 bonds, 2 residues, 1 model selected
> select up
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add /B2:415@OE2
20 atoms, 17 bonds, 3 residues, 1 model selected
> select up
28 atoms, 25 bonds, 3 residues, 1 model selected
> select add /P:389@NE2
29 atoms, 25 bonds, 4 residues, 1 model selected
> select up
38 atoms, 35 bonds, 4 residues, 1 model selected
> view sel
> select clear
> hbonds (#1/B2:410, P:85)
3 hydrogen bonds found
> hbonds (#1/ P:85, B2:410)
4 hydrogen bonds found
> hbonds (#1/ P:85-B2:410)
228 hydrogen bonds found
> ~hbonds
> select /B2:415@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
11 atoms, 9 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
5 hydrogen bonds found
> ~hbonds
> ui tool show H-Bonds
> hbonds sel color #000000 interModel false intraModel false saltOnly true
> intraRes false select true reveal true
0 hydrogen bonds found
> ui tool show H-Bonds
> select /B2:415@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /P:389@ND1
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 intraModel false saltOnly true intraRes false
> select true reveal true
0 hydrogen bonds found
> select /B2:415@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
11 atoms, 9 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both intraModel false saltOnly true
> intraRes false select true reveal true
0 hydrogen bonds found
> select /B2:415@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /P:389@CE1
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
Restriction atom specifier must not be blank
> ui tool show H-Bonds
> hbonds sel color #000000 restrict cross saltOnly true select true reveal
> true
1 hydrogen bonds found
> ~hbonds
> select up
4 atoms, 1 bond, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 restrict both saltOnly true select true reveal true
1 hydrogen bonds found
> select clear
> select /B2:415@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /P:389@ND1
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true select true reveal true
2 hydrogen bonds found
> select clear
> ~hbonds
> select /B2:415@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /P:389@ND1
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
7 hydrogen bonds found
> ~hbonds
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true intraMol false intraRes false select
> true reveal true
1 hydrogen bonds found
> select clear
> select /P:85@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /B2:410@OD1
12 atoms, 10 bonds, 2 residues, 1 model selected
> select up
19 atoms, 17 bonds, 2 residues, 1 model selected
> select up
281 atoms, 283 bonds, 37 residues, 1 model selected
> select down
19 atoms, 17 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true intraMol false intraRes false select
> true reveal true
0 hydrogen bonds found
> select /B2:413@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /P:86
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 4 atom styles
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> show sel atoms
[Repeated 9 time(s)]
> select /P:85@NH2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /P:86
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
211 atoms, 214 bonds, 26 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select /B2:410@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /P:86@N
9 atoms, 7 bonds, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true intraMol false intraRes false select
> true reveal true
0 hydrogen bonds found
> select /B2:410@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select /B2:404@CA
1 atom, 1 residue, 1 model selected
> select add /B2:403@CD
2 atoms, 2 residues, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select /B2:415@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /P:389@NE2
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true intraMol false intraRes false select
> true reveal true
1 hydrogen bonds found
> select add /B2:410@OD2
3 atoms, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add /P:86@N
28 atoms, 25 bonds, 4 residues, 1 model selected
> select up
31 atoms, 28 bonds, 4 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true intraMol false intraRes false select
> true reveal true
1 hydrogen bonds found
> hbonds sel reveal true
2 hydrogen bonds found
> ~hbonds
> select /B2:404@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select /P:86@N
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add /B2:415@OE1
5 atoms, 3 bonds, 2 residues, 1 model selected
> select up
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add /P:389@NE2
14 atoms, 11 bonds, 3 residues, 1 model selected
> select up
23 atoms, 21 bonds, 3 residues, 1 model selected
> select up
434 atoms, 443 bonds, 57 residues, 1 model selected
> select down
23 atoms, 21 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true intraMol false intraRes false select
> true reveal true
1 hydrogen bonds found
> select add /B2:410@OD2
3 atoms, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 saltOnly true intraMol false intraRes false select
> true reveal true
1 hydrogen bonds found
> select add /B2:410@OD2
3 atoms, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> select up
29 atoms, 26 bonds, 4 residues, 1 model selected
> select up
31 atoms, 28 bonds, 4 residues, 1 model selected
> hbonds sel reveal true
8 hydrogen bonds found
> select add /B2:413@CD
32 atoms, 28 bonds, 5 residues, 1 model selected
> select up
42 atoms, 38 bonds, 5 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
> select /B2:413@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B2:403@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B2:404@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /P:403
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /P:85
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /P:402
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add /P:85
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel cartoons
[Repeated 10 time(s)]
> hide sel cartoons
> show sel cartoons
> select clear
> select /P:86
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> ui tool show H-Bonds
> select add /B2:410@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /P:86@N
9 atoms, 7 bonds, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> hbonds sel color #000000 dashes 6 showDist true saltOnly true intraMol false
> intraRes false select true reveal true retainCurrent true
0 hydrogen bonds found
> ui tool show Contacts
> ui tool show H-Bonds
> hbonds sel color #0433ff dashes 6 saltOnly true intraMol false intraRes
> false select true reveal true retainCurrent true
Atom specifier selects no atoms
> select add /B2:410@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /P:86@N
9 atoms, 7 bonds, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0433ff dashes 6 saltOnly true intraMol false intraRes
> false select true reveal true retainCurrent true
0 hydrogen bonds found
> select clear
> ~hbonds
> select /B2:410@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /P:86@N
9 atoms, 7 bonds, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0433ff dashes 6 restrict both saltOnly true intraMol false
> intraRes false select true reveal true retainCurrent true
0 hydrogen bonds found
> select /B2:410@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /P:86@N
9 atoms, 7 bonds, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add /B2:415@OE2
13 atoms, 10 bonds, 3 residues, 1 model selected
> select up
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add /P:389@ND1
22 atoms, 18 bonds, 4 residues, 1 model selected
> select up
31 atoms, 28 bonds, 4 residues, 1 model selected
> hbonds sel
8 hydrogen bonds found
> hbonds sel color black
8 hydrogen bonds found
> select clear
> save Esx4_interaction_1.png supersample 8 transparentBackground true width
> 2400 height 2400
> transparency #1/B2, P 20 target c
> save Esx4_interaction_2.png supersample 8 transparentBackground true width
> 2400 height 2400
> transparency #1/B2, P 0 target c
> save Esx4_interaction_3.png supersample 8 transparentBackground true width
> 2400 height 2400
> transparency #1/B2, P 20 target c
> save Esx4_interaction_4.png supersample 8 transparentBackground true width
> 2400 height 2400
> size stickRadius 0.5
Changed 51678 bond radii
> size stickRadius 0.3
Changed 51678 bond radii
> size stickRadius 0.2
Changed 51678 bond radii
> size stickRadius 0.1
Changed 51678 bond radii
> size stickRadius 0.3
Changed 51678 bond radii
> size stickRadius 0.2
Changed 51678 bond radii
> save /Users/zchen/Desktop/contacts-hbond.cxs includeMaps true
> select
> /B2:8-27,37-64,98-105,143-146,210-215,228-232,256-258,288-298,310-314,324-326,352-354,432-438,449-454,463-466
852 atoms, 849 bonds, 113 residues, 1 model selected
> select /B2:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B2:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select
> /B2:8-27,37-64,98-105,143-146,210-215,228-232,256-258,288-298,310-314,324-326,352-354,432-438,449-454,463-466
852 atoms, 849 bonds, 113 residues, 1 model selected
> select /B2:24
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B2:23-24
15 atoms, 15 bonds, 2 residues, 1 model selected
> select /B2:23
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:23
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B2:21-22
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /B2:23
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:22-23
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /B2:23-24
15 atoms, 15 bonds, 2 residues, 1 model selected
> select /B2:23
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /B2:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B2:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain /D1
Alignment identifier is 1/D1
> ui tool show "Show Sequence Viewer"
> sequence chain /D2
Alignment identifier is 1/D2
> select
> /D2:38-53,63-66,85-88,130-156,163-184,189-208,217-238,242-265,269-295,343-378,389-412,416-440,442-468,473-488,490-498,500-505
2155 atoms, 2167 bonds, 309 residues, 1 model selected
> select /D2:289-290
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /D2:289-290
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /D2:289
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D2:289
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
Drag select of 2 residues
> select /B2:22@CG
1 atom, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> ui mousemode right select
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select /B2:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /D2:289
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /B2:22
20 atoms, 18 bonds, 2 residues, 1 model selected
> transparency #1/B2, D2 20 target c
> hbonds sel color black
3 hydrogen bonds found
> ~hbonds
> ui tool show "Side View"
> select /D2:289
11 atoms, 10 bonds, 1 residue, 1 model selected
> save Esx4_interaction_5.png supersample 8 transparentBackground true width
> 2400 height 2400
> ui tool show "Show Sequence Viewer"
> sequence chain /C1
Alignment identifier is 1/C1
> select /C1:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C2
Alignment identifier is 1/C2
> select /C2:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C2:200
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 13 residues
> select /C2:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /D4:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /D2:290
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C1
Alignment identifier is 1/C1
> select /C1:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select /D3:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel sphere
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C1:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
Drag select of 2 residues
> transparency #1/C1, D3 20 target c
> select /D3:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C1:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D3:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /C1:200
19 atoms, 17 bonds, 2 residues, 1 model selected
> hbonds sel color black
8 hydrogen bonds found
> ~hbonds
> ui tool show H-Bonds
> hbonds sel color #0433ff dashes 6 restrict both intraModel false saltOnly
> true intraMol false intraRes false select true reveal true retainCurrent
> true
0 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel color #0433ff dashes 6 restrict both interModel false intraModel
> false saltOnly true intraMol false intraRes false select true reveal true
> retainCurrent true
Atom specifier selects no atoms
> select /C1:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /D3:112@CB
12 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0433ff dashes 6 restrict both intraModel false saltOnly
> true intraMol false intraRes false select true reveal true retainCurrent
> true
0 hydrogen bonds found
> save Esx4_interaction_6.png supersample 8 transparentBackground true width
> 2400 height 2400
> select /C1:583
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:583
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /E1 /E2
Alignment identifier is 1
> select /E1:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select /C1:568
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:568
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:563
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:563
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:562
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:562
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:584
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C1:583-584
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /C1:583
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C1:583
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel cartoons
[Repeated 1 time(s)]
> show sel atoms
[Repeated 2 time(s)]
> show sel cartoons
> select /C1:584
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C1:583
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C1:581
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select /E1:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency #1/E1 C1 20 target c
Missing or invalid "percent" argument: Expected a number
> transparency #1/E1, C1 20 target c
> transparency #1/C1, E1 20 target c
> transparency #1/C1 20 target c
> select /C1:581
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /E1:94
19 atoms, 17 bonds, 2 residues, 1 model selected
> hbonds sel color black
2 hydrogen bonds found
> ~hbonds
> select /C1:581
11 atoms, 10 bonds, 1 residue, 1 model selected
> save Esx4_interaction_7.png supersample 8 transparentBackground true width
> 2400 height 2400
> select /C1:81
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /C1:81
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select /C2:81
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select /B1
3645 atoms, 3719 bonds, 492 residues, 1 model selected
> cartoon hide sel
> select /B2
3508 atoms, 3579 bonds, 472 residues, 1 model selected
> cartoon hide sel
> select /D1
3314 atoms, 3376 bonds, 2 pseudobonds, 464 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select /D2
3116 atoms, 3176 bonds, 2 pseudobonds, 435 residues, 2 models selected
> cartoon hide (#!1 & sel)
> transparency #1/C1, C2 20 target c
> save Esx4_interaction_7.png supersample 9 transparentBackground true width
> 2400 height 2400
> select /P
3172 atoms, 3249 bonds, 434 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /P
Alignment identifier is 1/P
> select /B2
3508 atoms, 3579 bonds, 472 residues, 1 model selected
> cartoon sel
> select /B1
3645 atoms, 3719 bonds, 492 residues, 1 model selected
> cartoon sel
> select /B2
3508 atoms, 3579 bonds, 472 residues, 1 model selected
> cartoon sel
> select /C1
9744 atoms, 9944 bonds, 1 pseudobond, 1271 residues, 2 models selected
> cartoon (#!1 & sel)
> select /C2
9737 atoms, 9937 bonds, 1 pseudobond, 1270 residues, 2 models selected
> select /C2
9737 atoms, 9937 bonds, 1 pseudobond, 1270 residues, 2 models selected
> cartoon (#!1 & sel)
> save /Users/zchen/Desktop/ESX-4-model_2.cxs includeMaps true
——— End of log from Tue Jun 24 16:09:32 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> show sel cartoons
[Repeated 1 time(s)]
> select up
50650 atoms, 51678 bonds, 8 pseudobonds, 6782 residues, 2 models selected
> select clear
> cartoon style width 2 thickness 2
> transparency 0 target c
> show cartoons
> graphics silhouettes false
> graphics silhouettes true
[Repeated 1 time(s)]
> save /Users/zchen/Desktop/Esx4_cartoon_1.png supersample 8 width 2400 height
> 2400 transparentBackground true
> turn x 90
[Repeated 2 time(s)]
> save /Users/zchen/Desktop/Esx4_cartoon_bottom_1.png supersample 8 width 2400
> height 2400 transparentBackground true
Unsupported scale factor (0.000000) detected on Display2
[Repeated 2 time(s)]
> ui tool show "Side View"
> ui tool show "Show Sequence Viewer"
> sequence chain /E1 /E2
Alignment identifier is 1
Could not find virtual screen for QCocoaScreen(0x6000016b5ad0, "DELL P2720D
(2)", QRect(0,0 2560x1440), dpr=1, displayId=94, <NSScreen: 0x6000004de580>)
with displayId 94
> select /E1-E2:93
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E1-E2:94
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E1-E2:94
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel red
> select /E1-E2:489
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E1-E2:489
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E1-E2:492
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /E1-E2:491-492
26 atoms, 24 bonds, 4 residues, 1 model selected
> select /E1-E2:491
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E1-E2:491
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel red
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, 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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, 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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, 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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, 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,
866,
695,
0,
0,
866,
695,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 278, in _draw_scene
offscreen.finish(r)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1867, in finish
cfb.copy_from_framebuffer(fb, depth=False)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2414, 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,
866,
695,
0,
0,
866,
695,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py", line 113, in _redraw
self.render()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py", line 288, in render
self.view.draw()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 278, in _draw_scene
offscreen.finish(r)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1867, in finish
cfb.copy_from_framebuffer(fb, depth=False)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2414, 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,
573,
59,
0,
0,
573,
59,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
Error processing trigger "frame drawn":
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glBlitFramebuffer,
cArguments = (
0,
0,
573,
59,
0,
0,
573,
59,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
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, 23 hours, 7 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
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: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → glClear: invalid framebuffer operation |
comment:2 by , 5 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Failed drawing status line during an expose event. Maybe this is related to the user having 2 external screens connected to MacBookAir. The QOpenGLContext has a "screen" attribute that is set when the context is created. Maybe if ChimeraX is moved to a different screen that sometimes creates a problem. When making the context current it passes the window for rendering, so Qt should know the window is on a new screen. Certainly it can't give this error whenever you move ChimeraX to a different screen on Mac or it would be reported often.