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#15344 closed defect (can't reproduce)
Could not make opengl context current
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\ihuman\APJ\β arrestin\manusccript\fig\20240508\apj barr
> interface.cxs" format session
Log from Wed May 8 13:59:06 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:\ihuman\APJ\β arrestin\manusccript\fig\20240508\overall model.cxs"
> format session
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #2, grid size 256,256,256,
pixel 1.04, shown at level 0.208, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #3.1, grid size 256,256,256,
pixel 1.04, shown at level 0.208, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #3.2, grid size 256,256,256,
pixel 1.04, shown at level 0.147, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #4, grid size 256,256,256,
pixel 1.04, shown at level 0.252, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #5.1, grid size 256,256,256,
pixel 1.04, shown at level 0.252, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #5.2, grid size 256,256,256,
pixel 1.04, shown at level 0.188, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #6, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #9.1, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #9.2, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #10, grid size 256,256,256,
pixel 1.04, shown at level 0.357, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #11.1, grid size
256,256,256, pixel 1.04, shown at level 0.357, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #11.2, grid size
256,256,256, pixel 1.04, shown at level 0.307, step 1, values float32
Log from Wed May 8 09:25:57 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/overall map.cxs"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #2, grid size 256,256,256,
pixel 1.04, shown at level 0.208, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #3.1, grid size 256,256,256,
pixel 1.04, shown at level 0.208, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #3.2, grid size 256,256,256,
pixel 1.04, shown at level 0.147, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #4, grid size 256,256,256,
pixel 1.04, shown at level 0.252, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #5.1, grid size 256,256,256,
pixel 1.04, shown at level 0.252, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #5.2, grid size 256,256,256,
pixel 1.04, shown at level 0.188, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #6, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #9.1, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #9.2, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #10, grid size 256,256,256,
pixel 1.04, shown at level 0.357, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #11.1, grid size
256,256,256, pixel 1.04, shown at level 0.357, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #11.2, grid size
256,256,256, pixel 1.04, shown at level 0.307, step 1, values float32
Log from Wed May 8 09:20:35 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/ihuman/APJ/β arrestin/structures/final/apjr_beta_fit86_cyc2.pdb"
Chain information for apjr_beta_fit86_cyc2.pdb #1
---
Chain | Description
C | No description available
H | No description available
L | No description available
R | No description available
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #2, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #2 level 0.2076
> set bgColor white
> select /R:240
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
329 atoms, 335 bonds, 40 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> color sel #537fc0ff
> select clear
> select /R:259
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
329 atoms, 335 bonds, 40 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.24
> ui tool show "Color Zone"
> color zone #2 near #1 distance 1.04
> color zone #2 near sel distance 1.04
[Repeated 1 time(s)]
> color zone #2 near sel distance 2.41
> color zone #2 near sel distance 3.25
> surface dust #2 size 10.4
> select clear
No atoms selected for color zoning
[Repeated 1 time(s)]
> select clear
> select /R:192
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
80 atoms, 80 bonds, 11 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> color zone #2 near sel distance 2.87
> color zone #2 near sel distance 2.68
> color zone #2 near sel distance 2.33
> color zone #2 near sel distance 3.31
> color zone #2 near sel distance 3.14
> surface dust #2 size 10.4
> volume splitbyzone #2
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #3.1, grid size 256,256,256,
pixel 1.04, shown at level 0.208, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #3.2, grid size 256,256,256,
pixel 1.04, shown at level 0.208, step 1, values float32
> hide #!3 models
> show #!3 models
> hide #!3 models
> select /C:320
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
104 atoms, 104 bonds, 13 residues, 1 model selected
> select up
2820 atoms, 2883 bonds, 355 residues, 1 model selected
> color sel #ca8ebaff
> color sel #eea219ff
> color sel #7899b2ff
> color sel #9ec46bff
> color sel #41aa81ff
> color sel #fe9fc5ff
> color sel #ca8ebaff
> select clear
> lighting soft
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #4, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #4 level 0.2518
> surface dust #4 size 10.4
> select #4
2 models selected
> select clear
> select /C:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
100 atoms, 104 bonds, 13 residues, 1 model selected
> select up
2820 atoms, 2883 bonds, 355 residues, 1 model selected
> color zone #4 near sel distance 6.24
> hide #!3.2 models
> hide #!3.1 models
> hide #!4 models
> show #!4 models
> color zone #4 near sel distance 2.46
> surface dust #4 size 10.4
> color zone #4 near sel distance 3.14
> volume splitbyzone #4
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #5.1, grid size 256,256,256,
pixel 1.04, shown at level 0.252, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #5.2, grid size 256,256,256,
pixel 1.04, shown at level 0.252, step 1, values float32
> show #!3.2 models
> volume #3.2 level 0.1913
> select add #3.2
2820 atoms, 2883 bonds, 355 residues, 3 models selected
> surface dust #3.2 size 10.4
> select subtract #3.2
2820 atoms, 2883 bonds, 355 residues, 1 model selected
> select clear
> hide #!1 models
> volume #5.2 level 0.2369
> surface dust #3.2 size 10.4
> surface dust #5.2 size 10.4
> show #!1 models
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #6, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #6 level 0.298
> select /L:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 8 residues, 1 model selected
> select up
817 atoms, 835 bonds, 107 residues, 1 model selected
> select up
7166 atoms, 7348 bonds, 898 residues, 1 model selected
> select down
817 atoms, 835 bonds, 107 residues, 1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 3 maps.
> hide #!6 models
> select add /H:49
828 atoms, 845 bonds, 108 residues, 1 model selected
> select up
882 atoms, 901 bonds, 115 residues, 1 model selected
> select up
1740 atoms, 1783 bonds, 226 residues, 1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 3 maps.
[Repeated 1 time(s)]
> select add #6
1740 atoms, 1783 bonds, 226 residues, 3 models selected
> color zone #6 near sel & #1 distance 6.24
> volume #6 level 0.3399
> color zone #6 near sel distance 6.24
> color zone #6 near sel distance 2.73
> color zone #6 near sel distance 1.58
> color single #6
> color zone #6 near sel distance 1.58
> color single #6
> select clear
> select /H:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 10 residues, 1 model selected
> select up
923 atoms, 948 bonds, 119 residues, 1 model selected
> select up
7166 atoms, 7348 bonds, 898 residues, 1 model selected
> select down
923 atoms, 948 bonds, 119 residues, 1 model selected
> select add #1
7166 atoms, 7348 bonds, 3 pseudobonds, 898 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #6
2 models selected
> select clear
> select /H:15
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 10 residues, 1 model selected
> select up
923 atoms, 948 bonds, 119 residues, 1 model selected
> select up
7166 atoms, 7348 bonds, 898 residues, 1 model selected
> select down
923 atoms, 948 bonds, 119 residues, 1 model selected
> select add /L:9
930 atoms, 955 bonds, 120 residues, 1 model selected
> select up
978 atoms, 1003 bonds, 127 residues, 1 model selected
> select up
1740 atoms, 1783 bonds, 226 residues, 1 model selected
> select up
7166 atoms, 7348 bonds, 898 residues, 1 model selected
> select down
1740 atoms, 1783 bonds, 226 residues, 1 model selected
> color zone #6 near sel & #1 distance 6.24
> color sel byhetero
[Repeated 1 time(s)]
> color zone #6 near sel distance 1.58
> color single #6
> color zone #6 near sel distance 1.58
> color zone #6 near sel distance 2.33
> volume #6 color #f1ce9f
> color zone #6 near sel distance 2.25
[Repeated 1 time(s)]
> color single #6
> close #6
> select clear
> select add #1
7166 atoms, 7348 bonds, 3 pseudobonds, 898 residues, 2 models selected
> select clear
> select add #1
7166 atoms, 7348 bonds, 3 pseudobonds, 898 residues, 2 models selected
> hide #!2 models
> select clear
> show #!2 models
> select #2
2 models selected
> select clear
> select /L:9
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 8 residues, 1 model selected
> select up
817 atoms, 835 bonds, 107 residues, 1 model selected
> select add /H:123
823 atoms, 840 bonds, 108 residues, 1 model selected
> select up
843 atoms, 860 bonds, 111 residues, 1 model selected
> select up
1740 atoms, 1783 bonds, 226 residues, 1 model selected
> color zone #2 near sel & #1 distance 6.24
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #6, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #6 level 0.1512
> color zone #6 near sel distance 6.24
> color zone #6 near sel distance 4.3
[Repeated 1 time(s)]
> volume splitbyzone #6
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #7.1, grid size 256,256,256,
pixel 1.04, shown at level 0.151, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #7.2, grid size 256,256,256,
pixel 1.04, shown at level 0.151, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 2 as #7.3, grid size 256,256,256,
pixel 1.04, shown at level 0.151, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 3 as #7.4, grid size 256,256,256,
pixel 1.04, shown at level 0.151, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 4 as #7.5, grid size 256,256,256,
pixel 1.04, shown at level 0.151, step 1, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3.2 models
> hide #!3.2 models
> show #!4 models
> hide #!4 models
> volume #6 level 0.8308
> volume #6 level 1.498
> volume #6 level 0.298
> surface dust #3.2 size 10.4
> surface dust #5.2 size 10.4
> surface dust #6 size 10.4
> volume #5.2 level 0.1884
> volume #6 level 0.3232
> volume #6 level 0.2854
> volume #7.2 color #f1ce9f
> volume #7.4 color #f1ce9f
> volume #7.5 color #f1ce9f
> volume #7.5 level 0.09533
> volume #7.5 level 0.06741
> volume #7.4 level 0.9053
> volume #7.2 level 0.2765
> surface dust #3.2 size 10.4
> surface dust #5.2 size 10.4
> surface dust #7.2 size 10.4
> surface dust #7.3 size 10.4
> surface dust #7.5 size 10.4
> undo
> volume #7.2 level 0.2009
> volume #7.3 level 0.1501
> close #7.3
> close #7.2
> close #7.4
> close #7.5
> close #7.1
> show #!1 models
> select clear
> select /H:95
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
923 atoms, 948 bonds, 119 residues, 1 model selected
> select up
7166 atoms, 7348 bonds, 898 residues, 1 model selected
> select down
923 atoms, 948 bonds, 119 residues, 1 model selected
> select add /L:9
930 atoms, 955 bonds, 120 residues, 1 model selected
> select up
978 atoms, 1003 bonds, 127 residues, 1 model selected
> select up
1740 atoms, 1783 bonds, 226 residues, 1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 3 maps.
> color zone #6 near sel distance 4.3
[Repeated 1 time(s)]
> volume splitbyzone #6
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #8.1, grid size 256,256,256,
pixel 1.04, shown at level 0.285, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #8.2, grid size 256,256,256,
pixel 1.04, shown at level 0.285, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 2 as #8.3, grid size 256,256,256,
pixel 1.04, shown at level 0.285, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 3 as #8.4, grid size 256,256,256,
pixel 1.04, shown at level 0.285, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 4 as #8.5, grid size 256,256,256,
pixel 1.04, shown at level 0.285, step 1, values float32
> volume #8.2 color #f1ce9f
> volume #8.4 color #f1ce9f
> volume #8.4 level 0.06314
> volume #8.5 color #f1ce9f
> volume #8.5 level 0.2938
> volume #8.1 level 1.756
> volume #8.2 level 0.1468
> volume #8.3 level 0.2351
> volume #8.4 level 0.08804
> select add #8
1740 atoms, 1783 bonds, 226 residues, 12 models selected
> select subtract #8
1740 atoms, 1783 bonds, 226 residues, 1 model selected
> select add #8
1740 atoms, 1783 bonds, 226 residues, 12 models selected
> surface dust #8.1 size 10.4
> surface dust #8.2 size 10.4
> surface dust #8.3 size 10.4
> surface dust #8.4 size 10.4
> volume #8.2 level 0.1396
> volume #8.3 level 0.1669
> volume #8.4 level 0.1556
> volume #8.5 level 0.07604
> close #8.1
> close #8.2
> close #8.3
> close #8.4
> close #8.5
> close #6
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #6, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #6 level 0.2393
> surface dust #3.2 size 10.4
> surface dust #5.2 size 10.4
> surface dust #6 size 10.4
> volume #6 level 0.6294
> select clear
[Repeated 1 time(s)]
> select /L:11
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 8 residues, 1 model selected
> select up
817 atoms, 835 bonds, 107 residues, 1 model selected
> select add /H:17
824 atoms, 842 bonds, 108 residues, 1 model selected
> select up
875 atoms, 893 bonds, 117 residues, 1 model selected
> select up
1740 atoms, 1783 bonds, 226 residues, 1 model selected
> color sel #add8e6ff
> color sel #7fbad5ff
> select clear
[Repeated 3 time(s)]
> select /H:13
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 10 residues, 1 model selected
> select up
923 atoms, 948 bonds, 119 residues, 1 model selected
> select add /L:17
927 atoms, 951 bonds, 120 residues, 1 model selected
> select up
964 atoms, 988 bonds, 125 residues, 1 model selected
> select up
1740 atoms, 1783 bonds, 226 residues, 1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 3 maps.
> select add #6
1740 atoms, 1783 bonds, 226 residues, 3 models selected
> color zone #6 near sel distance 6.24
> color zone #6 near sel distance 2.21
> color zone #6 near sel distance 21.59
> color zone #6 near sel distance 21.45
> color zone #6 near sel distance 21.3
> color zone #6 near sel distance 2.68
> volume #6 level 0.3357
> select #6
2 models selected
> select clear
> select #6
2 models selected
> select clear
> volume #6 level 0.2602
> volume #6 level 0.3022
> volume splitbyzone #6
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #9.1, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #9.2, grid size 256,256,256,
pixel 1.04, shown at level 0.302, step 1, values float32
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #10, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #10 level 0.5707
> select #5.2
2 models selected
> select clear
> select /R:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
193 atoms, 197 bonds, 17 residues, 1 model selected
> color sel #537fc0ff
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 4 maps.
> color zone #10 near sel distance 6.24
> volume #10 level 0.3483
> volume #10 level 0.3567
> color zone #10 near sel distance 6.24
> volume splitbyzone #10
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #11.1, grid size
256,256,256, pixel 1.04, shown at level 0.357, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #11.2, grid size
256,256,256, pixel 1.04, shown at level 0.357, step 1, values float32
> select add #1
7166 atoms, 7348 bonds, 3 pseudobonds, 898 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> volume #11.2 level 0.3069
> volume #3.2 level 0.1954
> volume #3.2 level 0.1466
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/overall map.cxs"
——— End of log from Wed May 8 09:20:35 2024 ———
opened ChimeraX session
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/overall map.png"
> width 1000 height 1090 supersample 4
> show #!1 models
> hide #!3.2 models
> hide #!5 models
> hide #!9.2 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #!11 models
> hide #!11.2 models
> ui tool show "Side View"
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/overall model.cxs"
——— End of log from Wed May 8 09:25:57 2024 ———
opened ChimeraX session
> select ::name="8EH"
37 atoms, 40 bonds, 1 residue, 1 model selected
> show sel atoms
> hide pseudobonds target p
> color sel #ffaa7fff
> style sel sphere
Changed 37 atom styles
> select ::name="CLR"
28 atoms, 31 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #b5b5b5ff
> select clear
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/overall model.png"
> width 1000 height 1090 supersample 4
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/overall model.cxs"
> lighting soft
> open "D:/ihuman/APJ/β arrestin/manusccript/fig/TM density/cmpd644.pdb"
> select add #12
37 atoms, 40 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select #1/R:401@C24
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> style sel stick
Changed 37 atom styles
> color sel #ffaa7fff
> color sel #ffaa00ff
> color sel #ffaa7fff
> color sel #ffaa00ff
> color sel #ffaa7fff
> select clear
> color #12 #ffaa7fff
> color byhetero
> select #1/R:401@C9
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> select up
193 atoms, 197 bonds, 17 residues, 1 model selected
> select down
37 atoms, 40 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> color zone #2 near sel & #1 distance 6.24
> volume #2 level 0.3628
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show "Color Zone"
> color zone #2 near #1 distance 1.04
> hide #!2 models
> show #!2 models
> color zone #2 near sel distance 1.04
> color zone #2 near sel distance 4.98
> hide #!2 models
> close #5.2
> close #9.1
> close #10
> close #11.2
> close #11.1
> close #9.2
> close #6
> close #5.1
> close #4
> close #3.2
> close #3.1
> close #2
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #2, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #2 level 0.3076
> color zone #2 near sel & #1 distance 6.24
> close #2
> show #3 models
> hide #3 models
> show #3 models
> show #5 models
> hide #3 models
> hide #5 models
> hide #12 models
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #2, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #2 level 0.2415
> select clear
> color zone #2 near #1 distance 6.24
> surface dust #2 size 10.4
> hide #!2 models
> color #!1 byhetero
[Repeated 1 time(s)]
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> show #!2 models
> color zone #2 near #1 distance 6.24
> select add #2
2 models selected
> hide #!2 target m
[Repeated 1 time(s)]
> close #2
> select add #3
1 model selected
> close
> open "D:/ihuman/APJ/β arrestin/structures/final/apjr_beta_fit86_cyc2.pdb"
Chain information for apjr_beta_fit86_cyc2.pdb #1
---
Chain | Description
C | No description available
H | No description available
L | No description available
R | No description available
> open "D:/ihuman/APJ/β
> arrestin/structures/final/cryosparc_P37_J106_map_sharp_hand.mrc"
Opened cryosparc_P37_J106_map_sharp_hand.mrc as #2, grid size 256,256,256,
pixel 1.04, shown at level 0.000134, step 1, values float32
> volume #2 level 0.1909
> select ::name="8EH"
37 atoms, 40 bonds, 1 residue, 1 model selected
> style sel stick
Changed 37 atom styles
> show sel atoms
> color sel #ffaa00ff
> color sel #ffaa7fff
> select clear
> color zone #2 near #1 distance 6.24
> select /R:401@C24
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> select up
193 atoms, 197 bonds, 17 residues, 1 model selected
> select down
37 atoms, 40 bonds, 1 residue, 1 model selected
> ui tool show "Color Zone"
> color zone #2 near #1 distance 1.04
> color zone #2 near sel distance 1.04
> color zone #2 near sel distance 3.82
> surface dust #2 size 10.4
> color zone #2 near sel distance 2.99
> color zone #2 near sel distance 2.37
> volume splitbyzone #2
Opened cryosparc_P37_J106_map_sharp_hand.mrc 0 as #3.1, grid size 256,256,256,
pixel 1.04, shown at level 0.191, step 1, values float32
Opened cryosparc_P37_J106_map_sharp_hand.mrc 1 as #3.2, grid size 256,256,256,
pixel 1.04, shown at level 0.191, step 1, values float32
> open "D:/ihuman/APJ/β arrestin/manusccript/fig/TM density/cmpd644.pdb"
> select add #4
74 atoms, 80 bonds, 2 residues, 2 models selected
> select subtract #4
37 atoms, 40 bonds, 1 residue, 1 model selected
> hide #!1 models
> select add #1
7166 atoms, 7348 bonds, 3 pseudobonds, 898 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!3.1 models
> surface dust #3.2 size 10.4
No atoms selected for color zoning
> volume #3.2 level 0.05465
> transparency #3.2.1 50
> volume #!3.2 style surface
> transparency #3.2.1 0
> transparency #3.2.1 50
> lighting soft
> lighting simple
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> volume #3.2 color #b5b5b580
> volume #3.2 color #ffffff80
> volume #3.2 color #b5b5b580
> color #4 #ffaa7fff
> color #4 byhetero
> transparency #3.2.1 0
> transparency #3.2.1 50
> surface dust #3.2 size 10.4
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/TM density/644.cxs"
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/TM density/644.png" width
> 1000 height 1130 supersample 4
[Repeated 1 time(s)]
> show #!1 models
> select #1/R:204
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
317 atoms, 328 bonds, 40 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> select down
317 atoms, 328 bonds, 40 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> select #3.2
2 models selected
> select #1/R:204
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
317 atoms, 328 bonds, 40 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> select down
317 atoms, 328 bonds, 40 residues, 1 model selected
> color #1 #537fc0ff
> select clear
> hide pseudobonds target p
> select #1/R:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
232 atoms, 237 bonds, 31 residues, 1 model selected
> hide sel cartoons
> select #1/R:83
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
217 atoms, 223 bonds, 28 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> select down
217 atoms, 223 bonds, 28 residues, 1 model selected
> hide sel cartoons
> select #1/C:230
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
116 atoms, 116 bonds, 14 residues, 1 model selected
> select up
2820 atoms, 2883 bonds, 355 residues, 1 model selected
> hide sel cartoons
> select #1/R:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
50 atoms, 52 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1/R:91
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
75 atoms, 79 bonds, 8 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> select down
75 atoms, 79 bonds, 8 residues, 1 model selected
> hide sel cartoons
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/644 in cartoon.png"
> width 1000 height 1130 supersample 4
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/644 in cartoon.cxs"
> hide pseudobonds target p
> hide #4 models
> hide #!3.2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> color sel byhetero
> color sel #ffaa00ff
> color sel #ffaa7fff
> color sel byhetero
> select clear
> select #1/H:62
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
43 atoms, 45 bonds, 4 residues, 1 model selected
> select up
923 atoms, 948 bonds, 119 residues, 1 model selected
> hide sel cartoons
> select #1/R:116
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
269 atoms, 276 bonds, 33 residues, 1 model selected
> select up
2420 atoms, 2491 bonds, 301 residues, 1 model selected
> show sel cartoons
> open 7W0M
Summary of feedback from opening 7W0M fetched from pdb
---
note | Fetching compressed mmCIF 7w0m from
http://files.rcsb.org/download/7w0m.cif
7w0m title:
Cryo-EM structure of a monomeric GPCR-Gi complex with small molecule [more
info...]
Chain information for 7w0m #5
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 1-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 32-102
R | Soluble cytochrome b562,Apelin receptor | C562_ECOLX -104-0, APJ_HUMAN
2-330
S | scFv16 |
Non-standard residues in 7w0m #5
---
8EH —
(1R,2S)-N-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-
propane-2-sulfonamide
> select clear
> select add #5
8929 atoms, 9125 bonds, 3 pseudobonds, 1135 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #2
2 models selected
> hide target m
> close #2
> close #3.1
> close #3.2
> select add #5
8929 atoms, 9125 bonds, 3 pseudobonds, 1135 residues, 2 models selected
> show #!5 models
> hide sel atoms
> show sel cartoons
> select clear
> show #!1 models
> split #5
Split 7w0m (#5) into 5 models
Chain information for 7w0m A #5.1
---
Chain | Description
A | No description available
Chain information for 7w0m B #5.2
---
Chain | Description
B | No description available
Chain information for 7w0m C #5.3
---
Chain | Description
C | No description available
Chain information for 7w0m R #5.4
---
Chain | Description
R | No description available
Chain information for 7w0m S #5.5
---
Chain | Description
S | No description available
> select add #5.4
2358 atoms, 2428 bonds, 291 residues, 1 model selected
> select subtract #5.4
Nothing selected
> select add #5.4
2358 atoms, 2428 bonds, 291 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!1 to #5.4
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 7w0m R, chain R (#5.4) with apjr_beta_fit86_cyc2.pdb, chain R (#1),
sequence alignment score = 1430.2
RMSD between 225 pruned atom pairs is 1.125 angstroms; (across all 290 pairs:
2.063)
> matchmaker #!1 to #5.4
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 7w0m R, chain R (#5.4) with apjr_beta_fit86_cyc2.pdb, chain R (#1),
sequence alignment score = 1430.2
RMSD between 225 pruned atom pairs is 1.125 angstroms; (across all 290 pairs:
2.063)
> select clear
> select #5.1/A:349
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
176 atoms, 177 bonds, 22 residues, 1 model selected
> select up
945 atoms, 964 bonds, 115 residues, 1 model selected
> select up
1015 atoms, 1034 bonds, 124 residues, 1 model selected
> select up
1378 atoms, 1408 bonds, 168 residues, 1 model selected
> select up
1387 atoms, 1416 bonds, 169 residues, 1 model selected
> select up
1758 atoms, 1787 bonds, 218 residues, 1 model selected
> hide sel cartoons
> select #5.2/B:81
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
55 atoms, 56 bonds, 6 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> select up
8929 atoms, 9125 bonds, 1135 residues, 5 models selected
> select down
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> select up
8929 atoms, 9125 bonds, 1135 residues, 5 models selected
> select down
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #5.3/C:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
138 atoms, 143 bonds, 18 residues, 1 model selected
> select up
418 atoms, 424 bonds, 55 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/L:87
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
60 atoms, 61 bonds, 7 residues, 1 model selected
> select up
817 atoms, 835 bonds, 107 residues, 1 model selected
> select up
7166 atoms, 7348 bonds, 898 residues, 1 model selected
> select down
817 atoms, 835 bonds, 107 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/R:432
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
193 atoms, 197 bonds, 17 residues, 1 model selected
> select up
2606 atoms, 2682 bonds, 317 residues, 1 model selected
> select down
193 atoms, 197 bonds, 17 residues, 1 model selected
> hide sel cartoons
> color #5.4 #fe9fc5ff
> color #5.4 #ca8ebaff
> color #5.4 #cebee3ff
> color #5.4 #fe9fc5ff
> color #5.4 #ff557fff
> color #5.4 #ff007fff
> color #5.4 #ff557fff
> color #5.4 #ffaaffff
> color #5.4 #ff5500ff
> color #5.4 #ff557fff
> color #5.4 #fe9fc5ff
> color #5.4 #ff557fff
> color #5.4 #ff007fff
> color #5.4 #ff557fff
Retrying to obtain clipboard.
[Repeated 1 time(s)]
Unable to obtain clipboard.
Retrying to obtain clipboard.
[Repeated 1 time(s)]
Unable to obtain clipboard.
Retrying to obtain clipboard.
[Repeated 1 time(s)]
Unable to obtain clipboard.
> cartoon style helix width 1.5 thickness 0.3
> cartoon style helix width 1.5 thickness 0.2
> cartoon style helix width 1.5 thickness 0.1
> cartoon style helix width 1.2 thickness 0.1
> cartoon style helix width 1.2 thickness 0.3
> select clear
> select #1/R:401@N4
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/barr vs Gpro.cxs"
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/barr vs Gpro.png"
> width 1000 height 1130 supersample 4
> select #5.5/S:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
241 atoms, 247 bonds, 31 residues, 1 model selected
> select up
1794 atoms, 1838 bonds, 233 residues, 1 model selected
> hide sel cartoons
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/barr vs Gpro top
> view.png" width 1000 height 1130 supersample 4
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/barr vs Gpro top
> view.cxs"
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/barr vs Gpro bottom
> view.cxs"
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/barr vs Gpro bottom
> view.png" width 1000 height 1130 supersample 4
> hide #5.4 models
> hide #5.3 models
> hide #5.2 models
> hide #!5.1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5.1 models
> hide #!5.1 models
> show #4 models
> hide #4 models
> show #3 models
> hide #3 models
> select ::name="8EH"
111 atoms, 120 bonds, 3 residues, 3 models selected
> show sel & #!1 atoms
> select clear
> hide #!5 models
> show #!5 models
> show #!5.1 models
> show #5.2 models
> show #5.3 models
> show #5.4 models
> hide #!5.5 models
> show #!5.5 models
> hide #!5.5 models
> show #!5.5 models
> select add #5.5
1794 atoms, 1838 bonds, 1 pseudobond, 233 residues, 2 models selected
> select subtract #5.5
Nothing selected
> select add #5
8929 atoms, 9125 bonds, 3 pseudobonds, 1135 residues, 8 models selected
> show sel cartoons
> select clear
> select add #5
8929 atoms, 9125 bonds, 3 pseudobonds, 1135 residues, 8 models selected
> show sel atoms
> hide sel atoms
> select subtract #5
Nothing selected
> select add #5
8929 atoms, 9125 bonds, 3 pseudobonds, 1135 residues, 8 models selected
> select subtract #5
Nothing selected
> select add #5.1
1758 atoms, 1787 bonds, 2 pseudobonds, 218 residues, 2 models selected
> select subtract #5.1
Nothing selected
> select add #5.2
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> select subtract #5.2
Nothing selected
> select add #5.3
418 atoms, 424 bonds, 55 residues, 1 model selected
> select subtract #5.3
Nothing selected
> select add #5.4
2358 atoms, 2428 bonds, 291 residues, 1 model selected
> select subtract #5.4
Nothing selected
> select add #5.5
1794 atoms, 1838 bonds, 1 pseudobond, 233 residues, 2 models selected
> select subtract #5.5
Nothing selected
> select add #5.1
1758 atoms, 1787 bonds, 2 pseudobonds, 218 residues, 2 models selected
> select subtract #5.1
Nothing selected
> select add #5.1
1758 atoms, 1787 bonds, 2 pseudobonds, 218 residues, 2 models selected
> select subtract #5.1
Nothing selected
> open 7w0m
7w0m title:
Cryo-EM structure of a monomeric GPCR-Gi complex with small molecule [more
info...]
Chain information for 7w0m #2
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 1-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 32-102
R | Soluble cytochrome b562,Apelin receptor | C562_ECOLX -104-0, APJ_HUMAN
2-330
S | scFv16 |
Non-standard residues in 7w0m #2
---
8EH —
(1R,2S)-N-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-
propane-2-sulfonamide
> hide #!2 models
> show #!2 models
> hide #5.2-4#!1-2#!5.1,5 atoms
> show #5.2-4#!1-2#!5.1,5 cartoons
> show #5.2-4#!1-2#!5.1,5 atoms
> select #5.4/R:85@NE1
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
222 atoms, 228 bonds, 28 residues, 1 model selected
> select up
2321 atoms, 2388 bonds, 290 residues, 1 model selected
> select down
222 atoms, 228 bonds, 28 residues, 1 model selected
> hide #!5 models
> hide #!5.1 models
> hide #5.2 models
> show #!5.1 models
> hide #!5.5 models
> hide #5.4 models
> hide #5.3 models
> show #5.4 models
> hide #!5.1 models
> hide #!5 models
> style #!1-2 stick
Changed 16095 atom styles
> select #2/B:50
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 6 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> select up
8929 atoms, 9125 bonds, 1135 residues, 1 model selected
> select down
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/H:61
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
43 atoms, 45 bonds, 4 residues, 1 model selected
> select up
923 atoms, 948 bonds, 119 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2/S:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
241 atoms, 247 bonds, 31 residues, 1 model selected
> select up
1794 atoms, 1838 bonds, 233 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/C:294
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
197 atoms, 197 bonds, 26 residues, 1 model selected
> select up
2820 atoms, 2883 bonds, 355 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select #2/A:216
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
36 atoms, 37 bonds, 4 residues, 1 model selected
> select up
433 atoms, 444 bonds, 53 residues, 1 model selected
> select up
450 atoms, 459 bonds, 55 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2/A:345
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
176 atoms, 177 bonds, 22 residues, 1 model selected
> select up
945 atoms, 964 bonds, 115 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2/A:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
200 atoms, 199 bonds, 26 residues, 1 model selected
> select up
380 atoms, 379 bonds, 50 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #1/L:56@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
96 atoms, 98 bonds, 13 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
> select #1/L:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
33 atoms, 32 bonds, 4 residues, 1 model selected
> select up
817 atoms, 835 bonds, 107 residues, 1 model selected
> select up
7166 atoms, 7348 bonds, 898 residues, 1 model selected
> select down
817 atoms, 835 bonds, 107 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/R:428@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
193 atoms, 197 bonds, 17 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #5.4 models
> select #2/R:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
276 atoms, 283 bonds, 34 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #2/R:78
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
124 atoms, 125 bonds, 17 residues, 1 model selected
> select up
2321 atoms, 2388 bonds, 290 residues, 1 model selected
> select down
124 atoms, 125 bonds, 17 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2/R:157
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
99 atoms, 100 bonds, 14 residues, 1 model selected
> select up
2321 atoms, 2388 bonds, 290 residues, 1 model selected
> select down
99 atoms, 100 bonds, 14 residues, 1 model selected
> select add #2/R:167
107 atoms, 107 bonds, 15 residues, 1 model selected
> select up
144 atoms, 146 bonds, 20 residues, 1 model selected
> select up
2321 atoms, 2388 bonds, 290 residues, 1 model selected
> select down
144 atoms, 146 bonds, 20 residues, 1 model selected
> select up
146 atoms, 147 bonds, 21 residues, 1 model selected
> select up
152 atoms, 153 bonds, 21 residues, 1 model selected
> select up
204 atoms, 206 bonds, 28 residues, 1 model selected
> select up
2321 atoms, 2388 bonds, 290 residues, 1 model selected
> select down
204 atoms, 206 bonds, 28 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 428 atoms, 90 residues, 361 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 35 atoms, 11 residues, 32 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 86 atoms, 23 residues, 75 bonds
> hide sel atoms
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
307 atoms, 317 bonds, 40 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 32 atoms, 5 residues, 32 bonds
> hide sel cartoons
> show sel atoms
> hide sel atoms
Drag select of 4 atoms, 1 residues, 4 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 45 atoms, 16 residues, 38 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 83 atoms, 20 residues, 75 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 29 atoms, 7 residues, 25 bonds
> select clear
Drag select of 44 atoms, 11 residues, 38 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 17 atoms, 3 residues, 13 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 15 atoms, 4 residues, 14 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 8 atoms, 1 residues, 7 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 4 atoms, 3 residues, 3 bonds
> hide sel cartoons
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
107 atoms, 107 bonds, 15 residues, 1 model selected
> select up
418 atoms, 424 bonds, 55 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #5.4 models
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select add #5.4
2776 atoms, 2852 bonds, 346 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show #!1 models
> select add #1
9942 atoms, 10200 bonds, 3 pseudobonds, 1244 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> undo
> select ::name="CLR"
28 atoms, 31 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="8EH"
148 atoms, 160 bonds, 4 residues, 4 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select clear
> select ::name="8EH"
148 atoms, 160 bonds, 4 residues, 4 models selected
> show sel & #5.4#!1-2 atoms
> select clear
> hide #5.4#!1-2 cartoons
> select #1/R:402@C9
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> color sel #9ec46bff
> color sel #55aa7fff
> color sel #9ec46bff
> select clear
> hide #!2 models
> color #5.4#!1 byhetero
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/644ligand
> compare.cxs"
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/644ligand
> compare.png" width 1000 height 1130 supersample 4
> hide #!5 models
> hide #5.4 models
> hide #!1 models
> show #!1 models
> show #!1 cartoons
> select #1/C:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
98 atoms, 98 bonds, 11 residues, 1 model selected
> select up
2820 atoms, 2883 bonds, 355 residues, 1 model selected
> color sel #fe9fc5ff
> select clear
> select #1/H:61
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
43 atoms, 45 bonds, 4 residues, 1 model selected
> select up
923 atoms, 948 bonds, 119 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/L:89
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
60 atoms, 61 bonds, 7 residues, 1 model selected
> select up
817 atoms, 835 bonds, 107 residues, 1 model selected
> hide sel cartoons
> cartoon style helix width 1.5 thickness 0.1
> cartoon style helix width 1.5 thickness 0.5
> cartoon style helix width 2.0 thickness 0.5
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 40 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 37 atom styles
> color sel byhetero
> select clear
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/apj barr
> interface.cxs"
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/apj barr
> interface.png" width 1000 height 1130 supersample 4
> select #1/C:128
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 1 model selected
> select up
2820 atoms, 2883 bonds, 355 residues, 1 model selected
> color sel #906ebdff
> color sel #ca8ebaff
> select clear
[Repeated 1 time(s)]
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/apj barr
> interface.png" width 1000 height 1130 supersample 4
> save "D:/ihuman/APJ/β arrestin/manusccript/fig/20240508/apj barr
> interface.cxs"
——— End of log from Wed May 8 13:59:06 2024 ———
opened ChimeraX session
[Repeated 1 time(s)]
OpenGL version: unknown
Could not make opengl context current
Python: 3.11.2
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: LENOVO
Model: 30ASA1J9CW
OS: Microsoft Windows 10 专业工作站版 (Build 19045)
Memory: 17,106,333,696
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
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: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (3)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unknown problem |
comment:2 by , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 17 months ago
| Summary: | Unknown problem → Could not make opengl context current |
|---|
The user opened a session and probably saw just a blank graphics pane, judging by the Report a Bug... dialog not being able to get any OpenGL info:
OpenGL version: unknown
Could not make opengl context current
That is probably what they are complaining about. Seems very likely to be a graphics driver problem. It puzzles me that if the OpenGL graphics failed it should have produced a traceback when trying to render the scene. So I'm not sure why we only see that in the bug report tool output.
Note:
See TracTickets
for help on using tickets.
I don't see any kind of error in this report.