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Opened 4 years ago
Closed 4 years ago
#5145 closed defect (can't reproduce)
Startup openGL errors
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/zsemersky/OneDrive - The College of Wooster/NA Summer 21/NADH
> Binding Site 2.cxs" format session
Could not find virtual screen for QCocoaScreen(0x600000b7c320, "Color LCD",
QRect(0,0 1680x1050), dpr=2, displayId=69734406, <NSScreen: 0x600001e42c40>)
with displayId 69734406
Log from Tue Aug 31 08:38:52 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zsemersky/Downloads/5eow.pdb format pdb
5eow.pdb title:
Crystal structure of 6-hydroxynicotinic acid 3-monooxygenase from pseudomonas
putida KT2440 [more info...]
Chain information for 5eow.pdb #1
---
Chain | Description
A | 6-hydroxynicotinate 3-monooxygenase
Non-standard residues in 5eow.pdb #1
---
FAD — flavin-adenine dinucleotide
> set bgColor white
> lighting simple
> hbonds reveal true
514 hydrogen bonds found
> hbonds reveal true
514 hydrogen bonds found
> ~hbonds
> interfaces ~solvent
0 buried areas:
> interfaces ~solvent
0 buried areas:
> ~hbonds
> hbonds reveal true
514 hydrogen bonds found
> ~hbonds
> show surfaces
> hide surfaces
> select :FAD
53 atoms, 58 bonds, 1 residue, 1 model selected
> show sel surfaces
> show sel surfaces
> hide sel surfaces
> select /A:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
42 atoms, 42 bonds, 5 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> show sel surfaces
> undo
> undo
> undo
> hide sel surfaces
> select /A:145@O
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
24 atoms, 23 bonds, 4 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> hide sel surfaces
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> select /A:273@CE3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select up
53 atoms, 55 bonds, 6 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 4 pseudobonds, 406 residues, 4 models selected
> select down
2828 atoms, 2846 bonds, 406 residues, 3 models selected
> select down
53 atoms, 55 bonds, 6 residues, 3 models selected
> hide sel surfaces
> show sel surfaces
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> hide sel surfaces
> hide (#!1 & sel) target a
> select /A:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting simple
> select /A
2828 atoms, 2846 bonds, 4 pseudobonds, 406 residues, 2 models selected
> show sel surfaces
> undo
> hide sel surfaces
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,2.9064,0,1,0,1.1574,0,0,1,-2.7402
> open /Users/zsemersky/Downloads/Conformer3D_CID_439153.sdf
PubChem entry 439153
> select clear
> select #2/?:1@O8
1 atom, 1 residue, 1 model selected
> select #2/?:1@O8
1 atom, 1 residue, 1 model selected
> view matrix models #2,1,0,0,0.59899,0,1,0,18.046,0,0,1,4.5937
> view matrix models #2,1,0,0,-21.233,0,1,0,60.39,0,0,1,55.173
> select clear
> select #2/?:1@C4
1 atom, 1 residue, 1 model selected
> view matrix models #2,1,0,0,-8.8938,0,1,0,71.557,0,0,1,35.157
> view matrix models #2,1,0,0,-7.1124,0,1,0,69.986,0,0,1,31.124
> view matrix models #2,1,0,0,-3.2467,0,1,0,61.787,0,0,1,30.997
> view matrix models #2,1,0,0,3.7374,0,1,0,61.845,0,0,1,25.308
> view matrix models #2,1,0,0,-2.3798,0,1,0,59.565,0,0,1,30.534
> view matrix models #2,1,0,0,-0.18468,0,1,0,60.926,0,0,1,28.87
> view matrix models #2,1,0,0,3.5254,0,1,0,60.704,0,0,1,26.827
> view matrix models #2,1,0,0,11.319,0,1,0,70.363,0,0,1,24.721
> ui mousemode right pivot
> select #2/?:1@P2
1 atom, 1 residue, 1 model selected
> select #2/?:1@H14
1 atom, 1 residue, 1 model selected
> select #2/?:1@C7
1 atom, 1 residue, 1 model selected
> select #2/?:1@P2
1 atom, 1 residue, 1 model selected
> select #2/?:1@O8
1 atom, 1 residue, 1 model selected
> select #2/?:1@P2
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
Drag select of 1 atoms
Drag select of 1 atoms
> undo
> ui mousemode right pivot
> select #2/?:1@H7
1 atom, 1 residue, 1 model selected
> select #2/?:1@O8
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select #1/A:346@CA
1 atom, 1 residue, 1 model selected
Alignment identifier is 1/A
> select
> #1/A:6-10,29-33,45-48,74-79,85-90,104-107,124-125,130-132,140-144,149-152,154-157,180-187,202-206,211-216,224-231,270-275,285-286,289-291
721 atoms, 730 bonds, 86 residues, 1 model selected
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select
> #1/A:6-10,29-33,45-48,74-79,85-90,104-107,124-125,130-132,140-144,149-152,154-157,180-187,202-206,211-216,224-231,270-275,285-286,289-291
721 atoms, 730 bonds, 86 residues, 1 model selected
Drag select of 5eow.pdb_A SES surface, 2445 of 277570 triangles, 13 atoms, 10
residues, 15 bonds
> select #1/A:281@CB
1 atom, 1 residue, 1 model selected
> select #1/A:281@CD2
1 atom, 1 residue, 1 model selected
> select #1/A:300@CE
1 atom, 1 residue, 1 model selected
> select #1/A:300@CE
1 atom, 1 residue, 1 model selected
> select #1/A:278@CA
1 atom, 1 residue, 1 model selected
> select #1/A:278@CB
1 atom, 1 residue, 1 model selected
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select
> #1/A:6-10,29-33,45-48,74-79,85-90,104-107,124-125,130-132,140-144,149-152,154-157,180-187,202-206,211-216,224-231,270-275,285-286,289-291
721 atoms, 730 bonds, 86 residues, 1 model selected
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select #1/A:300@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
54 atoms, 56 bonds, 7 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 4 pseudobonds, 406 residues, 4 models selected
> select down
2828 atoms, 2846 bonds, 406 residues, 3 models selected
> select down
54 atoms, 56 bonds, 7 residues, 3 models selected
> select down
9 atoms, 8 bonds, 1 residue, 2 models selected
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select #1/A:352@ND2
1 atom, 1 residue, 1 model selected
> select #1/A:349@CA
1 atom, 1 residue, 1 model selected
> select #1/A:349@OG
1 atom, 1 residue, 1 model selected
> select #1/A:345@OG
1 atom, 1 residue, 1 model selected
> select #1/A:280@CD
1 atom, 1 residue, 1 model selected
> select #1/A:283@CA
1 atom, 1 residue, 1 model selected
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select #1/A:170@CA
1 atom, 1 residue, 1 model selected
> select #1/A:334@CA
1 atom, 1 residue, 1 model selected
> select #1/A:341@NZ
1 atom, 1 residue, 1 model selected
> select #1/A:341@CB
1 atom, 1 residue, 1 model selected
> select #1/A:345@OG
1 atom, 1 residue, 1 model selected
> select #1/A:365@CB
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,3.1352,0,1,0,6.614,0,0,1,-9.2316
> ui mousemode right rotate
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,2.7844,0,1,0,5.4773,0,0,1,-4.5182
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select sequence H
150 atoms, 150 bonds, 15 residues, 1 model selected
> select sequence H
150 atoms, 150 bonds, 15 residues, 1 model selected
> select sequence H47
Nothing selected
> select sequence H47
Nothing selected
> select sequence 47H
Nothing selected
> select sequence H
150 atoms, 150 bonds, 15 residues, 1 model selected
> select sequence H
150 atoms, 150 bonds, 15 residues, 1 model selected
> view matrix models #1,1,0,0,-9.9888,0,1,0,3.9613,0,0,1,-13.094
> select #1/A:47@CD2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> color (#!1 & sel) cyan
> select clear
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select
> #1/A:6-10,29-33,45-48,74-79,85-90,104-107,124-125,130-132,140-144,149-152,154-157,180-187,202-206,211-216,224-231,270-275,285-286,289-291
721 atoms, 730 bonds, 86 residues, 1 model selected
> select
> #1/A:13-26,49-59,61-69,91-100,108-118,163-171,195-199,245-253,257-266,292-297,305-325,328-354,363-368
1106 atoms, 1111 bonds, 148 residues, 1 model selected
> select #1/A:105
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:105-109
40 atoms, 40 bonds, 5 residues, 1 model selected
> select
> #1/A:6-10,29-33,45-48,74-79,85-90,104-107,124-125,130-132,140-144,149-152,154-157,180-187,202-206,211-216,224-231,270-275,285-286,289-291
721 atoms, 730 bonds, 86 residues, 1 model selected
> select #1/A:81-112
249 atoms, 255 bonds, 32 residues, 1 model selected
> select #1/A:81-113
254 atoms, 260 bonds, 33 residues, 1 model selected
> select #1/A:113
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:112-113
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:112
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:106-107
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/A:108
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:107-108
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #1/A:107
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:107
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:47-48
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models #1,1,0,0,-3.7739,0,1,0,-5.363,0,0,1,-8.7409
> view matrix models #1,1,0,0,-0.68073,0,1,0,-9.6177,0,0,1,-7.2492
> view matrix models #1,1,0,0,-4.1073,0,1,0,-3.3027,0,0,1,-11.365
> ui mousemode right rotate
> ui mousemode right "move picked models"
> ui mousemode right translate
> select #1/A:286@NH1
1 atom, 1 residue, 1 model selected
> surface style #1.2 mesh
> surface style #1.2 solid
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select #1/A:47,215
22 atoms, 22 bonds, 2 residues, 1 model selected
> color (#!1 & sel) cyan
> select #1/A:215
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:215-216
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #1/A:216
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:215-216
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #1/A:215
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:215
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!1 & sel) orange
> color (#!1 & sel) magenta
> color (#!1 & sel) yellow
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate slab"
> ui mousemode right "move planes"
> ui mousemode right "pick blobs"
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,17.668,0,1,0,50.052,0,0,1,41.092
> view matrix models #2,1,0,0,14.847,0,1,0,51.069,0,0,1,39.872
> view matrix models #2,1,0,0,13.925,0,1,0,48.379,0,0,1,37.945
> view matrix models #2,1,0,0,17.439,0,1,0,44.637,0,0,1,38.516
> view matrix models #2,1,0,0,16.518,0,1,0,59.54,0,0,1,36.092
> view matrix models #2,1,0,0,15.706,0,1,0,47.617,0,0,1,44.969
> view matrix models #2,1,0,0,16.313,0,1,0,51.541,0,0,1,40.917
> color sel medium blue
> undo
> style sel stick
Changed 73 atom styles
> color sel lime
> style sel stick
Changed 73 atom styles
> style sel stick
Changed 73 atom styles
> style sel stick
Changed 73 atom styles
> color sel byhetero
> select #1/A:208@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
30 atoms, 29 bonds, 4 residues, 2 models selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> surface style #1.2 dot
> surface style #1.2 mesh
> surface style #1.2 dot
> surface hidePatches (#!1 & sel)
> surface style #1.2 mesh
> surface style #1.2 solid
> show sel surfaces
> surface style #1.2 mesh
> select #1/A:215
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:215
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel medium spring green
> color sel slate gray
> color sel cadet blue
> select #1/A:207@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> show sel surfaces
> surface style #1.2 solid
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel sienna
> color sel navy
> color sel medium violet red
> color sel dark orchid
> color sel blue violet
> color sel hot pink
> color sel medium slate blue
> color sel violet
> color sel magenta
> color sel deep pink
> color sel hot pink
> select #1/A:208@CB
1 atom, 1 residue, 1 model selected
> select #2/?:1@O7
1 atom, 1 residue, 1 model selected
> ui mousemode right "bond rotation"
> save "/Users/zsemersky/OneDrive - The College of Wooster/NA Summer 21/NicC
> Assn 2.cxs"
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> hide sel surfaces
> hbonds sel reveal true
478 hydrogen bonds found
> ui mousemode right translate
> ~hbonds
> select :FAD
53 atoms, 58 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
25 hydrogen bonds found
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
53 atoms, 58 bonds, 1 residue, 2 models selected
> select #1/A:182
5 atoms, 4 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byhetero
> select #1/A:163
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel surfaces
> select up
72 atoms, 71 bonds, 9 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> color (#!1 & sel) byhetero
> undo
> select #1/A:358
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:357-358
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:47,215
22 atoms, 22 bonds, 2 residues, 1 model selected
> color (#!1 & sel) byhetero
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> hide sel surfaces
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> ui tool show "Color Actions"
> color sel antique white
> color sel wheat
> color sel tan
> select clear
> lighting simple
> select #1/A:252
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> undo
> hide sel surfaces
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> show sel surfaces
> show sel surfaces
> select #1/A:278@CD
1 atom, 1 residue, 1 model selected
> select clear
> save "/Users/zsemersky/OneDrive - The College of Wooster/NA Summer
> 21/nicc.cxs"
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> hide sel surfaces
> show sel surfaces
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,18.953,0,1,0,49.046,0,0,1,41.033
> view matrix models #2,1,0,0,19.997,0,1,0,46.52,0,0,1,40.275
> view matrix models #2,1,0,0,11.332,0,1,0,52.856,0,0,1,40.331
> view matrix models #2,1,0,0,13.118,0,1,0,42.68,0,0,1,37.462
> view matrix models #2,1,0,0,13.806,0,1,0,42.48,0,0,1,36.43
> view matrix models #2,1,0,0,13.214,0,1,0,38.386,0,0,1,34.108
> view matrix models #2,1,0,0,12.16,0,1,0,38.378,0,0,1,34.64
> view matrix models #2,1,0,0,12.081,0,1,0,38.322,0,0,1,34.752
> view matrix models #2,1,0,0,-2.6887,0,1,0,54.395,0,0,1,24.297
> view matrix models #2,1,0,0,-6.5473,0,1,0,58.911,0,0,1,30.202
> view matrix models #2,1,0,0,-6.8699,0,1,0,67.322,0,0,1,34.375
> view matrix models #2,1,0,0,-5.3654,0,1,0,60.794,0,0,1,31.666
> view matrix models #2,1,0,0,-4.1737,0,1,0,60.116,0,0,1,31.154
> view matrix models #2,1,0,0,-0.78754,0,1,0,58.422,0,0,1,32.286
> select #1/A:278@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
82 atoms, 85 bonds, 9 residues, 2 models selected
> ui tool show "Color Actions"
> transparency (#!1 & sel) 20
> undo
> select up
82 atoms, 85 bonds, 9 residues, 2 models selected
> transparency (#!1 & sel) 0
> select
2901 atoms, 2923 bonds, 29 pseudobonds, 407 residues, 4 models selected
> select ::name="FAD"
53 atoms, 58 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select protein
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> select /A
2828 atoms, 2846 bonds, 29 pseudobonds, 406 residues, 3 models selected
> select clear
> select #1/A:273@CA
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select up
53 atoms, 55 bonds, 6 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 4 pseudobonds, 406 residues, 4 models selected
> select up
2828 atoms, 2846 bonds, 4 pseudobonds, 406 residues, 4 models selected
> select up
2901 atoms, 2923 bonds, 29 pseudobonds, 407 residues, 6 models selected
> select down
2828 atoms, 2846 bonds, 4 pseudobonds, 406 residues, 4 models selected
> select down
4 pseudobonds, 3 models selected
> select up
2776 atoms, 4 pseudobonds, 354 residues, 4 models selected
> select up
2828 atoms, 2846 bonds, 4 pseudobonds, 406 residues, 4 models selected
> select down
2776 atoms, 4 pseudobonds, 354 residues, 4 models selected
> hide sel surfaces
> show sel surfaces
> select #1/A:401@O2'
1 atom, 1 residue, 1 model selected
> select up
53 atoms, 58 bonds, 1 residue, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> select down
53 atoms, 58 bonds, 1 residue, 3 models selected
> hide sel surfaces
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> preset "initial styles" "space-filling (chain colors)"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show sel surfaces
> select #2/?:1@H15
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 1 model selected
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> show sel cartoons
> show sel atoms
> hide sel surfaces
> style sel stick
Changed 73 atom styles
> color (#!2 & sel) lime
> color (#!2 & sel) byhetero
> preset "initial styles" "space-filling (chain colors)"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style sel stick
Changed 73 atom styles
> color (#!2 & sel) lime
> color bfactor sel
73 atoms, 1 residues, 1 surfaces, atom bfactor range 0 to 0
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 73 atom styles
> show sel cartoons
> color (#!2 & sel) lime
> color (#!2 & sel) byhetero
> select #1/A:354@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
209 atoms, 211 bonds, 27 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> show sel surfaces
> select #1/A:401@PA
1 atom, 1 residue, 1 model selected
> select up
53 atoms, 58 bonds, 1 residue, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> select down
53 atoms, 58 bonds, 1 residue, 3 models selected
> hide sel surfaces
> ui tool show "Side View"
> view matrix models #1,1,0,0,-3.4502,0,1,0,0.85498,0,0,1,1.5736
> show sel atoms
> select #1/A:146@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
24 atoms, 23 bonds, 4 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> hbonds sel reveal true
514 hydrogen bonds found
> style sel stick
Changed 2828 atom styles
> hide sel atoms
> ~hbonds
> select :FAD
53 atoms, 58 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:211
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:211
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:211,302
20 atoms, 20 bonds, 2 residues, 1 model selected
> ui mousemode right distance
> show sel atoms
> color (#!1 & sel) byhetero
> color (#!1 & sel) magenta
> color (#!1 & sel) byhetero
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-0.80813,0,1,0,-0.26218,0,0,1,-7.5043
> ui mousemode right distance
> distance #1/A:211@NE2 #1/A:302@ND1
Distance between 5eow.pdb #1/A HIS 211 NE2 and HIS 302 ND1: 5.675Å
> ~distance #1/A:211@NE2 #1/A:302@ND1
> distance #1/A:302@ND1 #1/A:211@NE2
Distance between 5eow.pdb #1/A HIS 302 ND1 and HIS 211 NE2: 5.675Å
> ~distance #1/A:302@ND1 #1/A:211@NE2
> distance #1/A:302@ND1 #1/A:302@NE2
Distance between 5eow.pdb #1/A HIS 302 ND1 and NE2: 2.145Å
> ~distance #1/A:302@ND1 #1/A:302@NE2
> distance #1/A:302@NE2 #1/A:211@NE2
Distance between 5eow.pdb #1/A HIS 302 NE2 and HIS 211 NE2: 7.601Å
> ~distance #1/A:302@NE2 #1/A:211@NE2
> distance #1/A:302@NE2 #1/A:211@NE2
Distance between 5eow.pdb #1/A HIS 302 NE2 and HIS 211 NE2: 7.601Å
> ~distance #1/A:302@NE2 #1/A:211@NE2
> distance #1/A:302@NE2 #1/A:211@NE2
Distance between 5eow.pdb #1/A HIS 302 NE2 and HIS 211 NE2: 7.601Å
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,-2.6557,0,1,0,3.8178,0,0,1,-8.6763
> view matrix models #1,1,0,0,-3.3596,0,1,0,6.5059,0,0,1,-6.4006
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> view matrix models #1,1,0,0,-6.9305,0,1,0,9.7021,0,0,1,-2.5087
> select #2/?:1@N2
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> select down
1 model selected
> select #2/?:1@N2
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> view matrix models #1,1,0,0,-11.176,0,1,0,13.567,0,0,1,5.9831
> view matrix models #1,1,0,0,-9.1546,0,1,0,12.875,0,0,1,2.9548
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-7.7763,0,1,0,68.735,0,0,1,32.938
> view matrix models #2,1,0,0,-12.185,0,1,0,39.326,0,0,1,72.464
> view matrix models #2,1,0,0,-9.4329,0,1,0,27.418,0,0,1,39.56
> view matrix models #2,1,0,0,-13.381,0,1,0,41.273,0,0,1,14.638
> select #1/A:365
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
49 atoms, 52 bonds, 6 residues, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> show sel surfaces
> select #1/A:401@PA
1 atom, 1 residue, 1 model selected
> select up
53 atoms, 58 bonds, 1 residue, 2 models selected
> select up
2828 atoms, 2846 bonds, 406 residues, 2 models selected
> select down
53 atoms, 58 bonds, 1 residue, 3 models selected
> hide sel surfaces
> select clear
> select clear
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> view matrix models #2,1,0,0,-21.128,0,1,0,33.423,0,0,1,52.309
> view matrix models #2,1,0,0,-28.263,0,1,0,53.026,0,0,1,42.166
> view matrix models #2,1,0,0,-25.499,0,1,0,69.951,0,0,1,32.615
> view matrix models #2,1,0,0,-32.988,0,1,0,80.664,0,0,1,50.645
> view matrix models #2,1,0,0,-41.1,0,1,0,37.025,0,0,1,46.956
> view matrix models #2,1,0,0,1.0838,0,1,0,83.76,0,0,1,44.198
> view matrix models #2,1,0,0,4.3979,0,1,0,71.498,0,0,1,43.516
> view matrix models #2,1,0,0,-5.6038,0,1,0,71.217,0,0,1,43.145
> view matrix models #2,1,0,0,-5.3821,0,1,0,77.265,0,0,1,44.025
> view matrix models #2,1,0,0,-4.1683,0,1,0,83.972,0,0,1,45.398
> view matrix models #2,1,0,0,3.3277,0,1,0,93.987,0,0,1,52.532
> view matrix models #2,1,0,0,17.048,0,1,0,79.431,0,0,1,60.584
> view matrix models #2,1,0,0,15.878,0,1,0,81.079,0,0,1,60.316
> view matrix models #2,1,0,0,14.794,0,1,0,69.227,0,0,1,56.323
> view matrix models #2,1,0,0,13.838,0,1,0,65.739,0,0,1,55.095
> view matrix models #2,1,0,0,13.442,0,1,0,71.08,0,0,1,56.478
> hideH
Unknown command: hideH
> hide H
> view matrix models #2,1,0,0,13.852,0,1,0,69.239,0,0,1,56.903
> view matrix models #2,1,0,0,13.691,0,1,0,66.853,0,0,1,56.16
> select clear
Drag select of 5eow.pdb_A SES surface, 22311 of 277570 triangles, 63 atoms, 35
residues, 75 bonds, 1 pseudobonds
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> view matrix models #2,1,0,0,13.81,0,1,0,67.457,0,0,1,55.103
> view matrix models #2,1,0,0,13.786,0,1,0,67.272,0,0,1,54.769
> view matrix models #2,1,0,0,15.742,0,1,0,61.179,0,0,1,54.523
> view matrix models #2,1,0,0,12.432,0,1,0,64.918,0,0,1,54.108
> view matrix models #2,1,0,0,12.811,0,1,0,58.975,0,0,1,52.839
> view matrix models #2,1,0,0,13.712,0,1,0,48.946,0,0,1,51.136
> view matrix models #2,1,0,0,9.1234,0,1,0,51.288,0,0,1,48.75
> view matrix models #2,1,0,0,10.454,0,1,0,66.6,0,0,1,52.365
> view matrix models
> #2,0.2649,0.14893,0.9527,10.567,-0.3143,-0.92071,0.23132,66.865,0.91162,-0.36071,-0.19709,52.244
> view matrix models
> #2,0.65695,0.019458,-0.75369,10.828,0.23865,-0.95363,0.1834,66.596,-0.71517,-0.30035,-0.63113,53.188
> view matrix models
> #2,-0.23488,-0.94728,-0.21794,11.226,0.48341,-0.30835,0.81929,66.248,-0.84329,0.087078,0.53035,52.914
> view matrix models
> #2,0.49774,-0.69915,-0.51326,10.907,-0.22808,0.46544,-0.85519,66.989,0.8368,0.54273,0.072204,52.134
> view matrix models
> #2,-0.31815,0.45931,-0.82935,11.31,-0.72468,-0.68185,-0.099621,67.142,-0.61124,0.56932,0.54978,52.749
> view matrix models
> #2,-0.86174,-0.48728,-0.14126,11.488,0.32682,-0.74614,0.58006,66.429,-0.38805,0.45369,0.80223,52.577
> view matrix models
> #2,0.2776,-0.84286,0.46101,10.775,0.56706,-0.2436,-0.78683,66.624,0.77549,0.47984,0.41033,52.081
> view matrix models
> #2,0.2776,-0.84286,0.46101,9.9572,0.56706,-0.2436,-0.78683,60.28,0.77549,0.47984,0.41033,50.759
> view matrix models
> #2,0.2776,-0.84286,0.46101,11.505,0.56706,-0.2436,-0.78683,59.298,0.77549,0.47984,0.41033,50.939
> view matrix models
> #2,0.2776,-0.84286,0.46101,10.971,0.56706,-0.2436,-0.78683,52.278,0.77549,0.47984,0.41033,49.653
> view matrix models
> #2,0.2776,-0.84286,0.46101,8.041,0.56706,-0.2436,-0.78683,53.51,0.77549,0.47984,0.41033,49.593
> view matrix models
> #2,0.2776,-0.84286,0.46101,7.6595,0.56706,-0.2436,-0.78683,53.794,0.77549,0.47984,0.41033,49.242
> view matrix models
> #2,0.2776,-0.84286,0.46101,7.6084,0.56706,-0.2436,-0.78683,68.464,0.77549,0.47984,0.41033,52.225
> view matrix models
> #2,0.2776,-0.84286,0.46101,7.9607,0.56706,-0.2436,-0.78683,72.415,0.77549,0.47984,0.41033,55.284
> view matrix models
> #2,0.2776,-0.84286,0.46101,9.1397,0.56706,-0.2436,-0.78683,70.203,0.77549,0.47984,0.41033,55.082
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.2776,-0.84286,0.46101,29.437,0.56706,-0.2436,-0.78683,58.102,0.77549,0.47984,0.41033,41.58
> view matrix models
> #2,0.2776,-0.84286,0.46101,27.021,0.56706,-0.2436,-0.78683,56.5,0.77549,0.47984,0.41033,41.039
> view matrix models
> #2,0.2776,-0.84286,0.46101,28.388,0.56706,-0.2436,-0.78683,47.782,0.77549,0.47984,0.41033,43.163
> view matrix models
> #2,0.2776,-0.84286,0.46101,22.646,0.56706,-0.2436,-0.78683,44.687,0.77549,0.47984,0.41033,40.085
> view matrix models
> #2,0.2776,-0.84286,0.46101,30.819,0.56706,-0.2436,-0.78683,68.118,0.77549,0.47984,0.41033,53.384
> view matrix models
> #2,0.2776,-0.84286,0.46101,31.879,0.56706,-0.2436,-0.78683,68.679,0.77549,0.47984,0.41033,53.654
> view matrix models
> #2,0.2776,-0.84286,0.46101,26.823,0.56706,-0.2436,-0.78683,49.29,0.77549,0.47984,0.41033,43.073
> view matrix models
> #2,0.2776,-0.84286,0.46101,23.625,0.56706,-0.2436,-0.78683,47.075,0.77549,0.47984,0.41033,41.076
> view matrix models
> #2,0.2776,-0.84286,0.46101,19.617,0.56706,-0.2436,-0.78683,46.938,0.77549,0.47984,0.41033,39.633
> view matrix models
> #2,0.2776,-0.84286,0.46101,35.728,0.56706,-0.2436,-0.78683,62.674,0.77549,0.47984,0.41033,51.973
> ui mousemode right "bond rotation"
> select #2/?:1@O9
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@P1,O9,P2,O8 166.67
> torsion #2/?:1@C3,C9,O7,P1 -47.11
> torsion #2/?:1@C12,N2,C8,O2 51.55
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select #2/?:1@C10
1 atom, 1 residue, 1 model selected
> ui mousemode right "bond rotation"
> torsion #2/?:1@O2,C7,C10,O8 -170.95
> torsion #2/?:1@C12,N2,C8,O2 50.73
> select #2/?:1@P2
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@P1,O9,P2,O8 54.52
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select #2/?:1@C10
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@C7,C10,O8,P2 -174.47
> torsion #2/?:1@C12,N2,C8,O2 141.51
> torsion #2/?:1@C12,N2,C8,O2 175.05
> select clear
> torsion #2/?:1@O2,C7,C10,O8 128.13
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.2776,-0.84286,0.46101,32.761,0.56706,-0.2436,-0.78683,49.241,0.77549,0.47984,0.41033,45.165
> view matrix models
> #2,0.64546,0.19165,-0.73936,35.113,0.73064,-0.43703,0.52457,49.514,-0.22259,-0.87879,-0.42211,40.496
> view matrix models
> #2,-0.94056,0.057433,-0.33475,30.818,0.20232,-0.69691,-0.68803,47.638,-0.27281,-0.71486,0.64386,40.709
> view matrix models
> #2,-0.94056,0.057433,-0.33475,19.872,0.20232,-0.69691,-0.68803,43.451,-0.27281,-0.71486,0.64386,40.208
> view matrix models
> #2,-0.94056,0.057433,-0.33475,21.871,0.20232,-0.69691,-0.68803,43.371,-0.27281,-0.71486,0.64386,41.352
> view matrix models
> #2,-0.94056,0.057433,-0.33475,23.219,0.20232,-0.69691,-0.68803,44.662,-0.27281,-0.71486,0.64386,41.687
> ui mousemode right "bond rotation"
> select #2/?:1@O9
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@P1,O9,P2,O8 66.01
> select #2/?:1@P2
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@C10,O8,P2,O9 40.63
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@C12,N2,C8,O2 3.28
> torsion #2/?:1@O7,P1,O9,P2 156.85
> torsion #2/?:1@P1,O9,P2,O8 74.64
> torsion #2/?:1@C10,O8,P2,O9 71.28
> torsion #2/?:1@C10,O8,P2,O9 106.83
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> torsion #2/?:1@C10,O8,P2,O9 81.68
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.87497,0.39455,0.28065,24.694,-0.45687,-0.48083,-0.74838,43.002,-0.16033,-0.78303,0.60097,41.856
> view matrix models
> #2,-0.87248,0.40511,-0.27327,24.245,-0.081337,-0.67181,-0.73624,43.781,-0.48184,-0.62013,0.61909,41.213
> view matrix models
> #2,-0.72545,0.58431,0.36374,25.651,-0.50858,-0.098983,-0.85531,43.579,-0.46377,-0.80547,0.36898,40.649
> view matrix models
> #2,-0.8078,-0.39617,0.43647,23.316,-0.20934,-0.49938,-0.84071,43.662,0.55103,-0.7705,0.32046,43.884
> view matrix models
> #2,-0.8078,-0.39617,0.43647,24.943,-0.20934,-0.49938,-0.84071,41.965,0.55103,-0.7705,0.32046,39.994
> view matrix models
> #2,-0.8078,-0.39617,0.43647,26.364,-0.20934,-0.49938,-0.84071,43.402,0.55103,-0.7705,0.32046,41.508
> view matrix models
> #2,-0.8078,-0.39617,0.43647,19.141,-0.20934,-0.49938,-0.84071,43.273,0.55103,-0.7705,0.32046,41.494
> view matrix models
> #2,-0.8078,-0.39617,0.43647,18.642,-0.20934,-0.49938,-0.84071,45.907,0.55103,-0.7705,0.32046,40.561
> view matrix models
> #2,-0.8078,-0.39617,0.43647,19.504,-0.20934,-0.49938,-0.84071,46.775,0.55103,-0.7705,0.32046,40.022
> ui mousemode right "bond rotation"
> torsion #2/?:1@O2,C7,C10,O8 124.75
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.8078,-0.39617,0.43647,19.856,-0.20934,-0.49938,-0.84071,47.046,0.55103,-0.7705,0.32046,39.918
> view matrix models
> #2,-0.43883,-0.68591,-0.58047,19.523,-0.77559,0.61534,-0.14077,48.3,0.45374,0.38844,-0.80202,41.206
> view matrix models
> #2,-0.43883,-0.68591,-0.58047,18.038,-0.77559,0.61534,-0.14077,45.862,0.45374,0.38844,-0.80202,35.863
> view matrix models
> #2,-0.56779,-0.81568,0.11081,17.931,-0.50639,0.23999,-0.82823,45.306,0.64898,-0.52638,-0.54932,34.684
> view matrix models
> #2,-0.50057,-0.77625,-0.38323,17.812,-0.73413,0.61524,-0.28728,45.869,0.45878,0.13753,-0.87784,35.264
> view matrix models
> #2,-0.30164,-0.86739,-0.39579,18.227,-0.83679,0.4398,-0.32611,45.129,0.45694,0.23283,-0.85849,35.484
> view matrix models
> #2,-0.30164,-0.86739,-0.39579,25.603,-0.83679,0.4398,-0.32611,52.462,0.45694,0.23283,-0.85849,40.628
> view matrix models
> #2,-0.35312,-0.79501,-0.49322,25.518,-0.85139,0.49162,-0.18287,52.651,0.38786,0.35534,-0.85047,40.686
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.15918,-0.97708,-0.14133,26.025,-0.80584,0.2113,-0.55315,51.867,0.57033,0.025837,-0.82101,40.563
> view matrix models
> #2,-0.07989,-0.98115,-0.17596,26.237,-0.77788,0.17175,-0.60449,51.825,0.62331,0.088585,-0.77694,40.904
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.07989,-0.98115,-0.17596,24.029,-0.77788,0.17175,-0.60449,45.604,0.62331,0.088585,-0.77694,39.951
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.50228,-0.8451,-0.18307,22.993,-0.84078,0.52677,-0.12492,46.589,0.20201,0.091179,-0.97513,38.465
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.50228,-0.8451,-0.18307,22.76,-0.84078,0.52677,-0.12492,46.327,0.20201,0.091179,-0.97513,37.863
> view matrix models
> #2,-0.50228,-0.8451,-0.18307,30.761,-0.84078,0.52677,-0.12492,52.278,0.20201,0.091179,-0.97513,41.6
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.22257,-0.70215,0.67635,34.419,-0.97046,-0.22586,0.084883,50.509,0.093156,-0.67526,-0.73167,38.937
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.22257,-0.70215,0.67635,24.554,-0.97046,-0.22586,0.084883,44.016,0.093156,-0.67526,-0.73167,40.343
> view matrix models
> #2,0.22257,-0.70215,0.67635,21.483,-0.97046,-0.22586,0.084883,43.805,0.093156,-0.67526,-0.73167,39.676
Drag select of 5eow.pdb_A SES surface, 14 of 277570 triangles, 1 residues
> view matrix models
> #2,-0.92139,-0.21342,0.3248,18.66,-0.38852,0.52694,-0.7559,46.576,-0.0098278,-0.82267,-0.56843,39.167
> view matrix models
> #2,-0.92139,-0.21342,0.3248,27.846,-0.38852,0.52694,-0.7559,50.7,-0.0098278,-0.82267,-0.56843,44.904
> view matrix models
> #2,-0.8268,-0.54146,0.15239,27.279,-0.55512,0.82918,-0.065608,51.421,-0.090838,-0.13884,-0.98614,45.796
> view matrix models
> #2,-0.8268,-0.54146,0.15239,16.743,-0.55512,0.82918,-0.065608,46.637,-0.090838,-0.13884,-0.98614,38.71
> view matrix models
> #2,-0.8268,-0.54146,0.15239,19.17,-0.55512,0.82918,-0.065608,49.362,-0.090838,-0.13884,-0.98614,40.489
> view matrix models
> #2,-0.8268,-0.54146,0.15239,28.026,-0.55512,0.82918,-0.065608,58.742,-0.090838,-0.13884,-0.98614,53.724
> view matrix models
> #2,-0.8268,-0.54146,0.15239,26.75,-0.55512,0.82918,-0.065608,55.453,-0.090838,-0.13884,-0.98614,47.858
> view matrix models
> #2,-0.8268,-0.54146,0.15239,31.078,-0.55512,0.82918,-0.065608,62.013,-0.090838,-0.13884,-0.98614,50.142
> view matrix models
> #2,-0.8268,-0.54146,0.15239,27.472,-0.55512,0.82918,-0.065608,61.237,-0.090838,-0.13884,-0.98614,49.467
> select clear
> view matrix models
> #2,-0.70493,-0.64625,0.2923,27.743,-0.59544,0.76312,0.25118,61.232,-0.38539,0.0030156,-0.92275,48.905
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> view matrix models
> #2,-0.74067,-0.61857,0.26226,27.666,-0.59516,0.78518,0.1711,61.214,-0.31176,-0.02936,-0.94971,49.043
> view matrix models
> #2,-0.73882,-0.62216,0.25895,27.661,-0.5996,0.78229,0.16883,61.192,-0.30761,-0.030535,-0.95102,49.052
> view matrix models
> #2,-0.047634,0.54212,0.83895,32.876,0.71774,0.6027,-0.34871,64.504,-0.69468,0.58554,-0.41781,49.635
> view matrix models
> #2,-0.89603,0.43798,0.072833,29.334,-0.27568,-0.6774,0.68201,59.443,0.34805,0.59102,0.72771,53.893
> view matrix models
> #2,-0.89603,0.43798,0.072833,26.462,-0.27568,-0.6774,0.68201,49.599,0.34805,0.59102,0.72771,44.941
> view matrix models
> #2,-0.7912,0.11825,0.60002,26.536,-0.0088717,-0.98325,0.18207,49.346,0.6115,0.13873,0.77899,44.821
> view matrix models
> #2,-0.7912,0.11825,0.60002,28.242,-0.0088717,-0.98325,0.18207,50.869,0.6115,0.13873,0.77899,42.244
> view matrix models
> #2,-0.7673,-0.1183,0.63028,27.825,0.15724,-0.98754,0.0060723,51.233,0.62171,0.10376,0.77634,42.197
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,26.663,-0.040263,-0.83953,0.54181,51.389,-0.12669,0.54216,0.83067,40.85
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,24.131,-0.040263,-0.83953,0.54181,49.81,-0.12669,0.54216,0.83067,44.806
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.355,-0.040263,-0.83953,0.54181,47.881,-0.12669,0.54216,0.83067,43.968
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,18.03,-0.040263,-0.83953,0.54181,49.919,-0.12669,0.54216,0.83067,42.779
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,17.89,-0.040263,-0.83953,0.54181,49.943,-0.12669,0.54216,0.83067,42.685
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,17.202,-0.040263,-0.83953,0.54181,50.336,-0.12669,0.54216,0.83067,42.495
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,17.084,-0.040263,-0.83953,0.54181,50.959,-0.12669,0.54216,0.83067,42.431
> ui mousemode right translate
> ui mousemode right translate
> save "/Users/zsemersky/OneDrive - The College of Wooster/NA Summer 21/NicC
> binding assignment 1.cxs"
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,17.168,-0.040263,-0.83953,0.54181,51.429,-0.12669,0.54216,0.83067,42.936
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.969,-0.040263,-0.83953,0.54181,51.405,-0.12669,0.54216,0.83067,42.353
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,17.342,-0.040263,-0.83953,0.54181,51.55,-0.12669,0.54216,0.83067,42.252
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,17.491,-0.040263,-0.83953,0.54181,52.005,-0.12669,0.54216,0.83067,42.644
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.364,-0.040263,-0.83953,0.54181,51.626,-0.12669,0.54216,0.83067,42.584
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.739,-0.040263,-0.83953,0.54181,52.144,-0.12669,0.54216,0.83067,42.553
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.532,-0.040263,-0.83953,0.54181,51.874,-0.12669,0.54216,0.83067,42.639
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,15.872,-0.040263,-0.83953,0.54181,51.644,-0.12669,0.54216,0.83067,42.587
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.63,-0.040263,-0.83953,0.54181,52.246,-0.12669,0.54216,0.83067,42.808
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.236,-0.040263,-0.83953,0.54181,51.777,-0.12669,0.54216,0.83067,42.929
> save "/Users/zsemersky/OneDrive - The College of Wooster/NA Summer 21/NicC
> binding assignment 1.cxs"
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,16.243,-0.040263,-0.83953,0.54181,51.525,-0.12669,0.54216,0.83067,42.963
> ui mousemode right "bond rotation"
> torsion #2/?:1@C12,N2,C8,O2 88.71
> torsion #2/?:1@C12,N2,C8,O2 66.66
> select clear
> ui mousemode right translate
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:47
10 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue
> select #1/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:150-151
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/A:215
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:215
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue
> ui mousemode right distance
> ~distance #1/A:302@NE2 #1/A:211@NE2
> ui mousemode right translate
> select clear
> select #1/A:273@CZ3
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select #1/A:42@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #1/A:273@CH2
9 atoms, 7 bonds, 2 residues, 2 models selected
> select add #1/A:273@CZ3
10 atoms, 7 bonds, 2 residues, 2 models selected
> select add #1/A:273@CZ2
11 atoms, 7 bonds, 2 residues, 2 models selected
> select add #1/A:273@CE3
12 atoms, 7 bonds, 2 residues, 2 models selected
> select add #1/A:273@CD2
13 atoms, 7 bonds, 2 residues, 2 models selected
> select add #1/A:273@CE2
14 atoms, 7 bonds, 2 residues, 2 models selected
> select add #1/A:35@CG
15 atoms, 7 bonds, 3 residues, 2 models selected
> select add #1/A:35@CD
16 atoms, 7 bonds, 3 residues, 2 models selected
> select add #1/A:35@NE2
17 atoms, 7 bonds, 3 residues, 2 models selected
> select add #1/A:35@CB
18 atoms, 7 bonds, 3 residues, 2 models selected
> select add #1/A:35@O
19 atoms, 7 bonds, 3 residues, 2 models selected
> select add #1/A:36@CA
20 atoms, 7 bonds, 4 residues, 2 models selected
> select add #1/A:35@C
21 atoms, 7 bonds, 4 residues, 2 models selected
> select add #1/A:129@CB
22 atoms, 7 bonds, 5 residues, 2 models selected
> select add #1/A:129@NH1
23 atoms, 7 bonds, 5 residues, 2 models selected
> select add #1/A:129@N
24 atoms, 7 bonds, 5 residues, 2 models selected
> select add #1/A:35@CA
25 atoms, 7 bonds, 5 residues, 2 models selected
> transparency (#!1 & sel) 50
> transparency (#!1 & sel) 60
> select subtract #1/A:273@CH2
24 atoms, 7 bonds, 5 residues, 2 models selected
> select subtract #1/A:273@CZ3
23 atoms, 7 bonds, 5 residues, 2 models selected
> select add #1/A:273@CH2
24 atoms, 7 bonds, 5 residues, 2 models selected
> select add #1/A:273@CZ3
25 atoms, 7 bonds, 5 residues, 2 models selected
> select subtract #1/A:273@CZ3
24 atoms, 7 bonds, 5 residues, 2 models selected
> select subtract #1/A:273@CH2
23 atoms, 7 bonds, 5 residues, 2 models selected
> select #1/A:184@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> transparency (#!1 & sel) 60
> select clear
> save "/Users/zsemersky/OneDrive - The College of Wooster/NA Summer 21/NADH
> Binding Site 1.cxs"
> select #1/A:273@CH2
1 atom, 1 residue, 1 model selected
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> transparency (#!1 & sel) 0
> ui mousemode right select
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,7.1332,-0.040263,-0.83953,0.54181,67.268,-0.12669,0.54216,0.83067,57.122
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,11.48,-0.040263,-0.83953,0.54181,71.057,-0.12669,0.54216,0.83067,49.036
> view matrix models
> #2,-0.99113,-0.035196,-0.12819,37.141,-0.040263,-0.83953,0.54181,62.677,-0.12669,0.54216,0.83067,54.449
> ui mousemode right "bond rotation"
> torsion #2/?:1@C12,N2,C8,O2 63.47
> torsion #2/?:1@C7,C10,O8,P2 154.91
> torsion #2/?:1@C12,N2,C8,O2 -116.04
> select #2/?:1@O9
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@O7,P1,O9,P2 168.36
> torsion #2/?:1@P1,O9,P2,O8 117.31
> select #1/A:177@CB
1 atom, 1 residue, 1 model selected
Drag select of 5eow.pdb_A SES surface, 1133 of 277570 triangles, 8 residues, 1
bonds
> torsion #2/?:1@C3,C9,O7,P1 -49.12
> torsion #2/?:1@C9,O7,P1,O9 -67.29
> torsion #2/?:1@C9,O7,P1,O9 -171.43
> torsion #2/?:1@C10,O8,P2,O9 88.51
> torsion #2/?:1@C12,N2,C8,O2 -158.62
> torsion #2/?:1@C10,O8,P2,O9 104.91
> torsion #2/?:1@P1,O9,P2,O8 97.48
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,36.824,0.22134,-0.88642,0.40653,62.663,-0.26893,0.34522,0.89917,54.192
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,22.244,0.22134,-0.88642,0.40653,73.918,-0.26893,0.34522,0.89917,58.353
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,16.847,0.22134,-0.88642,0.40653,73.575,-0.26893,0.34522,0.89917,60.833
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,16.763,0.22134,-0.88642,0.40653,75.09,-0.26893,0.34522,0.89917,59.322
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,16.89,0.22134,-0.88642,0.40653,68.997,-0.26893,0.34522,0.89917,59.513
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,17.926,0.22134,-0.88642,0.40653,69.174,-0.26893,0.34522,0.89917,58.566
> select #1/A:231@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
67 atoms, 70 bonds, 8 residues, 2 models selected
> select #1/A:209@OD2
1 atom, 1 residue, 1 model selected
> select add #1/A:209@CB
2 atoms, 1 residue, 2 models selected
> select add #1/A:209@CG
3 atoms, 1 residue, 2 models selected
Drag select of 5eow.pdb_A SES surface, 111 of 277570 triangles, 2 residues
> select add #1/A:210@NH2
27 atoms, 4 residues, 2 models selected
> select subtract #1/A:210@NH2
26 atoms, 3 residues, 2 models selected
> select add #1/A:210@CZ
27 atoms, 4 residues, 2 models selected
> select add #1/A:210@NH2
28 atoms, 4 residues, 2 models selected
> select add #1/A:231@CG
29 atoms, 5 residues, 2 models selected
> select add #1/A:231@CB
30 atoms, 5 residues, 2 models selected
> select add #1/A:230@CG1
31 atoms, 6 residues, 2 models selected
> select add #1/A:231@O
32 atoms, 6 residues, 2 models selected
> select add #1/A:229@CA
33 atoms, 7 residues, 2 models selected
> select add #1/A:229@C
34 atoms, 7 residues, 2 models selected
> select add #1/A:229@O
35 atoms, 7 residues, 2 models selected
> select add #1/A:209@O
36 atoms, 7 residues, 2 models selected
> select add #1/A:230@N
37 atoms, 7 residues, 2 models selected
> select add #1/A:227@CG2
38 atoms, 8 residues, 2 models selected
> select add #1/A:227@CG1
39 atoms, 8 residues, 2 models selected
> select add #1/A:209@CA
40 atoms, 8 residues, 2 models selected
> select subtract #1/A:209@CA
39 atoms, 8 residues, 2 models selected
> select add #1/A:209@CA
40 atoms, 8 residues, 2 models selected
> select add #1/A:208@O
41 atoms, 9 residues, 2 models selected
> select add #1/A:208@CB
42 atoms, 9 residues, 2 models selected
> select add #1/A:231@N
43 atoms, 9 residues, 2 models selected
> select add #1/A:230@CA
44 atoms, 9 residues, 2 models selected
> select add #1/A:230@C
45 atoms, 9 residues, 2 models selected
> select add #1/A:231@CD
46 atoms, 9 residues, 2 models selected
> select subtract #1/A:231@CG
45 atoms, 9 residues, 2 models selected
> select subtract #1/A:231@N
44 atoms, 9 residues, 2 models selected
> select add #1/A:231@CG
45 atoms, 9 residues, 2 models selected
> select add #1/A:231@N
46 atoms, 9 residues, 2 models selected
> select add #1/A:231@CA
47 atoms, 9 residues, 2 models selected
> select add #1/A:45@O
48 atoms, 10 residues, 2 models selected
> select add #1/A:44@CB
49 atoms, 11 residues, 2 models selected
> select add #1/A:207@OG
50 atoms, 12 residues, 2 models selected
> select add #1/A:209@OD1
51 atoms, 12 residues, 2 models selected
> select add #1/A:210@CD
52 atoms, 12 residues, 2 models selected
> select add #1/A:208@N
53 atoms, 12 residues, 2 models selected
> select add #1/A:210@NE
54 atoms, 12 residues, 2 models selected
> select add #1/A:209@N
55 atoms, 12 residues, 2 models selected
> select subtract #1/A:209@OD1
54 atoms, 12 residues, 2 models selected
> select subtract #1/A:207@OG
53 atoms, 11 residues, 2 models selected
> select add #1/A:209@OD1
54 atoms, 11 residues, 2 models selected
> select add #1/A:207@OG
55 atoms, 12 residues, 2 models selected
> select add #1/A:210@CG
56 atoms, 12 residues, 2 models selected
> transparency (#!1 & sel) 70
> ui mousemode right select
> select clear
> select #2/?:1@C7
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,14.015,0.22134,-0.88642,0.40653,70.506,-0.26893,0.34522,0.89917,58.379
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,15.318,0.22134,-0.88642,0.40653,68.581,-0.26893,0.34522,0.89917,58.373
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,16.27,0.22134,-0.88642,0.40653,68.442,-0.26893,0.34522,0.89917,58.249
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,16.063,0.22134,-0.88642,0.40653,68.651,-0.26893,0.34522,0.89917,58.058
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,16.433,0.22134,-0.88642,0.40653,68.704,-0.26893,0.34522,0.89917,57.814
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,11.502,0.22134,-0.88642,0.40653,54.072,-0.26893,0.34522,0.89917,53.372
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,9.5058,0.22134,-0.88642,0.40653,57.102,-0.26893,0.34522,0.89917,49.511
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> hide sel surfaces
> view matrix models #1,1,0,0,-8.9595,0,1,0,13.018,0,0,1,2.8522
> select #2/?:1@O2
1 atom, 1 residue, 1 model selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> select up
73 atoms, 77 bonds, 1 residue, 2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,9.0789,0.22134,-0.88642,0.40653,54.985,-0.26893,0.34522,0.89917,49.439
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,9.504,0.22134,-0.88642,0.40653,55.45,-0.26893,0.34522,0.89917,49.025
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,10.025,0.22134,-0.88642,0.40653,54.215,-0.26893,0.34522,0.89917,47.798
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,9.8244,0.22134,-0.88642,0.40653,54.339,-0.26893,0.34522,0.89917,47.891
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> ui mousemode right "bond rotation"
> torsion #2/?:1@C12,N2,C8,O2 170.69
> select #1/A:209@CB
1 atom, 1 residue, 1 model selected
> select #1/A:209@CB
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@C7,C10,O8,P2 -63.84
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,7.965,0.22134,-0.88642,0.40653,54.37,-0.26893,0.34522,0.89917,48.44
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,7.282,0.22134,-0.88642,0.40653,54.378,-0.26893,0.34522,0.89917,48.922
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,7.2444,0.22134,-0.88642,0.40653,54.652,-0.26893,0.34522,0.89917,48.608
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,7.316,0.22134,-0.88642,0.40653,53.979,-0.26893,0.34522,0.89917,50.188
> ui mousemode right "bond rotation"
> select #2/?:1@O7
1 atom, 1 residue, 1 model selected
> select #2/?:1@O7
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@O2,C7,C10,O8 101.15
> select #2/?:1@C10
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@O7,P1,O9,P2 140.08
> ui mousemode right translate
> ui mousemode right select
> select clear
> select clear
> select clear
> ui mousemode right translate
> ui mousemode right "bond rotation"
> torsion #2/?:1@C7,C10,O8,P2 -42.77
> torsion #2/?:1@P1,O9,P2,O8 -166.79
> torsion #2/?:1@O2,C7,C10,O8 86.30
> select #2/?:1@C8
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.3964,0.22134,-0.88642,0.40653,54.432,-0.26893,0.34522,0.89917,50.314
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.3264,0.22134,-0.88642,0.40653,54.173,-0.26893,0.34522,0.89917,50.654
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.4795,0.22134,-0.88642,0.40653,54.297,-0.26893,0.34522,0.89917,50.308
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.4598,0.22134,-0.88642,0.40653,54.2,-0.26893,0.34522,0.89917,50.415
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.9126,0.22134,-0.88642,0.40653,54.458,-0.26893,0.34522,0.89917,49.822
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.9238,0.22134,-0.88642,0.40653,54.01,-0.26893,0.34522,0.89917,50.038
> ui mousemode right "bond rotation"
> torsion #2/?:1@O2,C7,C10,O8 89.16
> select #1/A:229@CA
1 atom, 1 residue, 1 model selected
> select #2/?:1@O9
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@P1,O9,P2,O8 174.18
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,7.2523,0.22134,-0.88642,0.40653,54.417,-0.26893,0.34522,0.89917,48.914
> ui mousemode right "bond rotation"
> torsion #2/?:1@O2,C7,C10,O8 82.89
> torsion #2/?:1@C7,C10,O8,P2 -44.61
> torsion #2/?:1@C10,O8,P2,O9 149.41
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.6366,0.22134,-0.88642,0.40653,54.807,-0.26893,0.34522,0.89917,48.858
> view matrix models
> #2,-0.93738,-0.30835,-0.16197,6.5772,0.22134,-0.88642,0.40653,54.646,-0.26893,0.34522,0.89917,49.091
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,6.3796,0.15747,-0.98628,0.049506,53.252,-0.53692,-0.043436,0.84252,47.012
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,5.5418,0.15747,-0.98628,0.049506,53.06,-0.53692,-0.043436,0.84252,47.82
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,5.4962,0.15747,-0.98628,0.049506,52.919,-0.53692,-0.043436,0.84252,47.947
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,5.1861,0.15747,-0.98628,0.049506,53.196,-0.53692,-0.043436,0.84252,47.897
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,5.1045,0.15747,-0.98628,0.049506,53.314,-0.53692,-0.043436,0.84252,47.903
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,5.1391,0.15747,-0.98628,0.049506,53.25,-0.53692,-0.043436,0.84252,47.914
> ui mousemode right "bond rotation"
> torsion #2/?:1@P1,O9,P2,O8 162.65
> torsion #2/?:1@H25,O11,P2,O8 44.77
> torsion #2/?:1@C10,O8,P2,O9 164.20
> torsion #2/?:1@C7,C10,O8,P2 -145.31
> select #2/?:1@N2
1 atom, 1 residue, 1 model selected
> torsion #2/?:1@C12,N2,C8,O2 -105.88
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,5.1966,0.15747,-0.98628,0.049506,53.316,-0.53692,-0.043436,0.84252,47.754
> view matrix models
> #2,-0.82881,-0.15925,-0.53639,5.2133,0.15747,-0.98628,0.049506,53.223,-0.53692,-0.043436,0.84252,47.841
> select #2/?:1@N2
1 atom, 1 residue, 1 model selected
> ui mousemode right "bond rotation"
> torsion #2/?:1@C12,N2,C8,O2 -133.37
> torsion #2/?:1@C12,N2,C8,O2 -132.25
> torsion #2/?:1@C12,N2,C8,O2 -132.25
> ui mousemode right translate
> ui mousemode right "bond rotation"
> torsion #2/?:1@C12,N2,C8,O2 -100.44
> torsion #2/?:1@O14,C20,C16,C12 152.62
> torsion #2/?:1@C12,N2,C8,O2 -120.28
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> transparency (#!1 & sel) 0
> ui tool show "Color Actions"
> color sel medium slate blue
> hide sel surfaces
> select clear
> select /A:5-376
2723 atoms, 2788 bonds, 4 pseudobonds, 353 residues, 2 models selected
> show sel surfaces
> select clear
> save "/Users/zsemersky/OneDrive - The College of Wooster/NA Summer 21/NADH
> Binding Site 2.cxs"
——— End of log from Tue Aug 31 08:38:52 2021 ———
opened ChimeraX session
Could not find virtual screen for QCocoaScreen(0x600000b7c320, "Color LCD",
QRect(0,0 1680x1050), dpr=2, displayId=69734406, <NSScreen: 0x600001e42c40>)
with displayId 69734406
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 82, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 148, in status
r.draw_background()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 82, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 148, in status
r.draw_background()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/seq_canvas.py", line 232, in _actually_resize
self._reformat()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/seq_canvas.py", line 968, in _reformat
self.sv.status("Reformatting alignment; please wait...", blank_after=0)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2022, in status
StatusLogger.status(self, *args, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py", line 196, in status
if l.status(msg, color, secondary) and getattr(l, "excludes_other_logs",
True):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 148, in status
r.draw_background()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> select #1/A:231@CG
1 atom, 1 residue, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1741, in _sel_change_cb
self.show_chimerax_selection()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1169, in
show_chimerax_selection
sv.status("ChimeraX selection region displayed.",
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2022, in status
StatusLogger.status(self, *args, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/logger.py", line 196, in status
if l.status(msg, color, secondary) and getattr(l, "excludes_other_logs",
True):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 148, in status
r.draw_background()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 1154, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Error processing trigger "selection changed":
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 11.5.2 (20G95)
Kernel Version: Darwin 20.6.0
Time since boot: 20:48
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Startup openGL errors |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Duplicate of #4367. Apparently a Mac Qt bug.
This bug report suggests it is related to a problem with Mac DisplayLink drivers.
https://github.com/spyder-ide/spyder/issues/12601