Startup openGL errors

[chimerax-bug-report@…]

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

[Tom Goddard]

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