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Opened 2 years ago
Closed 2 years ago
#10054 closed defect (not a bug)
"turn" arguments
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202310201838 (2023-10-20 18:38:44 UTC)
Description
Dear developers,
I run into a problem using turn command. I have an object that I need to rotate for movie away from me. When I tried "turn x 1 45" model rotated smoothly as it supposed with 1 deg step to 45 degree but this was rotation towards me. So I reversed sign to rotate opposite way:"turn x 1 -45"; got an error "Missing or invalid "frames" argument: Must be greater than or equal to 1", similar outcome if using "turn x -1 -45". It only works if I ask " turn x -45" but in this case it just jumps to 45 degree in desired direction, no smooth transition.
Is there any way around this problem?
Thank you!
Log:
UCSF ChimeraX version: 1.7.dev202310201838 (2023-10-20)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\grush\Documents\Seminars\Munc13
> project\Model_paper\Jim's_presentation\For_movie_ringSNARES.cxs" format
> session
Log from Tue Oct 24 00:42:49 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\grush\Documents\Seminars\Munc13
> project\Model_paper\Fig1_with_peripherals_green_movie.cxs" format session
Log from Thu Jun 29 11:41:30 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_with_peripherals_green_movie.cxs"
Log from Thu Jun 29 10:01:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #afeeee00
Log from Wed Jun 28 14:44:32 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\grush\Documents\Seminars\Munc13
> project\Model_paper\Fig1_with_peripherals.cxs" format session
Log from Wed Jun 28 13:03:52 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\grush\Documents\Seminars\Munc13
> project\Model_paper\Fig1_with_peripherals.cxs" format session
Log from Sat Jun 24 02:02:49 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\grush\Documents\Seminars\Munc13 project\Model_paper\Fig1.cxs"
> format session
Log from Fri Apr 21 11:53:23 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "C:\Users\grush\Documents\Seminars\Munc13 project\Model_paper\Fig1.cxs"
> format session
Log from Wed Mar 29 12:26:29 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "C:/Users/grush/Documents/Seminars/Munc13 project/Model_paper/Fig1.cxs"
Log from Wed Mar 29 11:09:51 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_MUN.pdb"
Summary of feedback from opening C:/Users/grush/Documents/Seminars/Munc13
project/Model_paper/Fig1_MUN.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 9
VAL A 21 1 13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
2 messages similar to the above omitted
Chain information for Fig1_MUN.pdb
---
Chain | Description
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B | No description available
> set bgColor pale turquoise
> open "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_SNAREpins.pdb"
> "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_Syt_ring.pdb"
Summary of feedback from opening C:/Users/grush/Documents/Seminars/Munc13
project/Model_paper/Fig1_SNAREpins.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 9
VAL A 21 1 13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
2 messages similar to the above omitted
Summary of feedback from opening C:/Users/grush/Documents/Seminars/Munc13
project/Model_paper/Fig1_Syt_ring.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 9
VAL A 21 1 13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
9 messages similar to the above omitted
CONECT record for nonexistent atom: 2613
Start residue of secondary structure not found: HELIX 1 1 VAL A 9 VAL A 21 1
13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
30 messages similar to the above omitted
Chain information for Fig1_SNAREpins.pdb
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A | No description available
2.1/B 2.2/B | No description available
2.3/B | No description available
2.4/B | No description available
2.1/C 2.3/C 2.4/C 2.5/C | No description available
2.2/C | No description available
2.6/C | No description available
2.1/D 2.2/D 2.3/D 2.4/D 2.5/D 2.6/D | No description available
2.1/E 2.2/E 2.3/E 2.4/E 2.5/E 2.6/E | No description available
Chain information for Fig1_Syt_ring.pdb
---
Chain | Description
3.2/F 3.3/F 3.4/F 3.5/F 3.6/F 3.7/F | No description available
3.1/G | No description available
3.1/Q | No description available
Drag select of 7232 residues, 81 pseudobonds, 7232 atoms
> hide sel atoms
> show sel cartoons
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> select clear
Drag select of 3564 residues, 48 pseudobonds
> color (#!1.1-6 & sel) dark gray
> select clear
> select #2:1213-1220
Nothing selected
> select #1:1213-1220
906 atoms, 906 bonds, 48 residues, 6 models selected
> color sel yellow
> select #1:1154-1169
1644 atoms, 1692 bonds, 96 residues, 6 models selected
> color sel yellow
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> color sel yellow
> select clear
> save "C:/Users/grush/Documents/Seminars/Munc13 project/Model_paper/Fig1.cxs"
> show #!1.1-6 surfaces
> hide #!1.1-6 surfaces
> show #!1.1-6 surfaces
> hide #!1.1-6 surfaces
Drag select of 3564 residues, 48 pseudobonds
> show sel surfaces
> color sel bypolymer
> show sel surfaces
> hide sel surfaces
> select clear
Drag select of 3564 residues, 48 pseudobonds
> color (#!1.1-6 & sel) gray
> color (#!1.1-6 & sel) light gray
> color (#!1.1-6 & sel) gray
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> color (#!1.1-6 & sel) yellow
> select #1:1154-1169
1644 atoms, 1692 bonds, 96 residues, 6 models selected
> color (#!1.1-6 & sel) yellow
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> select #1:1154-1169
1644 atoms, 1692 bonds, 96 residues, 6 models selected
> color (#!1.1-6 & sel) yellow
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> select #1:1154-1169
1644 atoms, 1692 bonds, 96 residues, 6 models selected
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> select #1:1154-1169
1644 atoms, 1692 bonds, 96 residues, 6 models selected
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> color (#!1.1-6 & sel) yellow
> select #1:1123-1140
1890 atoms, 1926 bonds, 108 residues, 6 models selected
> select #1:1213-1220
906 atoms, 906 bonds, 48 residues, 6 models selected
> color (#!1.1-6 & sel) yellow
> select clear
> show #!1.1-6 surfaces
[Repeated 1 time(s)]
> hide #!1.1-6 surfaces
> show #!1.1-6 surfaces
> ui tool show "Side View"
> hide #!1 models
> show #!3 models
Drag select of 113 residues, 3 pseudobonds
> select clear
Drag select of 114 residues, 3 pseudobonds
> select add #3.4/F:272
712 atoms, 8 bonds, 3 pseudobonds, 115 residues, 2 models selected
> select clear
Drag select of 114 residues, 3 pseudobonds
> select add #3.4/F:272
712 atoms, 8 bonds, 3 pseudobonds, 115 residues, 2 models selected
> select add #3.4/F:273
720 atoms, 15 bonds, 3 pseudobonds, 116 residues, 2 models selected
> delete sel
Drag select of 116 residues, 3 pseudobonds
> delete sel
Drag select of 116 residues, 3 pseudobonds
> delete sel
Drag select of 116 residues, 3 pseudobonds
> delete sel
Drag select of 113 residues, 3 pseudobonds
> delete sel
Drag select of 3 residues
> delete sel
Drag select of 115 residues, 3 pseudobonds
> select add #3.3/F:273
720 atoms, 7 bonds, 3 pseudobonds, 116 residues, 2 models selected
> delete sel
> show #!1 models
> select add #3.1/G:1992
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> hide #!1 models
> show #!2 models
> hide #!2 models
Drag select of 2611 residues
> color sel light gray
> show #!1 models
> hide #!1 models
> select clear
Drag select of 342 residues
> select up
3045 atoms, 3097 bonds, 383 residues, 2 models selected
> color sel yellow
> select clear
Drag select of 2611 residues
> show sel surfaces
> hide sel surfaces
Drag select of 2611 residues
> color (#!3.1-7 & sel) light gray
> select clear
Drag select of 348 residues
> select up
3137 atoms, 3190 bonds, 394 residues, 5 models selected
> select up
6950 atoms, 7088 bonds, 870 residues, 5 models selected
> select down
3137 atoms, 3190 bonds, 394 residues, 5 models selected
> color (#!3.1,5 & sel) yellow
> select clear
Drag select of 2611 residues
> show sel surfaces
> select clear
> show #!1 models
> select #3.4/F:283@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
77 atoms, 78 bonds, 9 residues, 2 models selected
> select up
1155 atoms, 1178 bonds, 145 residues, 2 models selected
> select up
1155 atoms, 1178 bonds, 145 residues, 2 models selected
> select up
1155 atoms, 1178 bonds, 145 residues, 2 models selected
> select #3.1/G:1990@CG2
1 atom, 1 residue, 1 model selected
> select add #3.1/Q:2038@CE2
2 atoms, 2 residues, 2 models selected
> select add #3.5/F:338@OH
3 atoms, 3 residues, 4 models selected
> select up
31 atoms, 30 bonds, 3 residues, 5 models selected
> select up
297 atoms, 300 bonds, 36 residues, 5 models selected
> select up
3473 atoms, 3542 bonds, 435 residues, 5 models selected
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> select clear
[Repeated 1 time(s)]
> hide #!1.1-6#!3.1-7 surfaces
Drag select of 16 residues
> select up
338 atoms, 337 bonds, 45 residues, 2 models selected
> select up
2318 atoms, 2364 bonds, 290 residues, 2 models selected
> color (#!3.1 & sel) yellow
> select clear
> select #3.1/G:1652
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
77 atoms, 76 bonds, 10 residues, 2 models selected
> select up
1159 atoms, 1182 bonds, 145 residues, 2 models selected
> color (#!3.1 & sel) light gray
> select clear
> show #!1.1-6#!3.1-7 surfaces
> show #!2 models
> hide #!2 models
> hide #!3 models
Drag select of Fig1_MUN.pdb_B SES surface, Fig1_MUN.pdb_B SES surface,
Fig1_MUN.pdb_B SES surface, Fig1_MUN.pdb_B SES surface, Fig1_MUN.pdb_B SES
surface, Fig1_MUN.pdb_B SES surface, 3564 residues, 48 pseudobonds
> show #!2 models
> show #!3 models
> save "C:/Users/grush/Documents/Seminars/Munc13 project/Model_paper/Fig1.cxs"
——— End of log from Wed Mar 29 11:09:51 2023 ———
opened ChimeraX session
> select add #1
57264 atoms, 57888 bonds, 54 pseudobonds, 3564 residues, 13 models selected
> select subtract #1.1
47720 atoms, 48240 bonds, 45 pseudobonds, 2970 residues, 17 models selected
> select subtract #1.2
38176 atoms, 38592 bonds, 36 pseudobonds, 2376 residues, 14 models selected
> select add #1
57264 atoms, 57888 bonds, 54 pseudobonds, 3564 residues, 17 models selected
> select subtract #1.3
47720 atoms, 48240 bonds, 45 pseudobonds, 2970 residues, 17 models selected
> select subtract #1.4
38176 atoms, 38592 bonds, 36 pseudobonds, 2376 residues, 14 models selected
> select add #1
57264 atoms, 57888 bonds, 54 pseudobonds, 3564 residues, 17 models selected
> select subtract #1
6 models selected
> hide #!3 models
> show #!3 models
> hide #!2 models
> ui tool show "Side View"
> hide #!1 models
> hide #!3.1-7 surfaces
Drag select of 62 residues
> select up
780 atoms, 789 bonds, 97 residues, 2 models selected
> select up
2318 atoms, 2364 bonds, 290 residues, 2 models selected
> select down
780 atoms, 789 bonds, 97 residues, 2 models selected
> select clear
Drag select of 76 residues
> select up
891 atoms, 899 bonds, 112 residues, 2 models selected
> select up
3477 atoms, 3546 bonds, 435 residues, 2 models selected
> select clear
Drag select of 68 residues
> select up
837 atoms, 846 bonds, 104 residues, 2 models selected
> select up
2318 atoms, 2364 bonds, 290 residues, 2 models selected
> color (#!3.1 & sel) #bdff72ff
> color (#!3.1 & sel) #c4ff6cff
> color (#!3.1 & sel) #dbff65ff
> color (#!3.1 & sel) #eeff59ff
> color (#!3.1 & sel) #f6ff52ff
> color (#!3.1 & sel) #fcff4aff
> color (#!3.1 & sel) #fff240ff
> color (#!3.1 & sel) #ffe839ff
> color (#!3.1 & sel) #ffe733ff
> color (#!3.1 & sel) #ffe72eff
> color (#!3.1 & sel) #ffe02eff
> color (#!3.1 & sel) #ffdc2eff
> color (#!3.1 & sel) #ffd22eff
> color (#!3.1 & sel) #ffcb2eff
> color (#!3.1 & sel) #ffc12fff
> color (#!3.1 & sel) #ffba2fff
> color (#!3.1 & sel) #ffb32fff
> color (#!3.1 & sel) #ffaf2fff
> color (#!3.1 & sel) #ffb32fff
> color (#!3.1 & sel) #ffc130ff
> color (#!3.1 & sel) #ffc531ff
> color (#!3.1 & sel) #ffcc33ff
> color (#!3.1 & sel) #ffd333ff
> color (#!3.1 & sel) #ffd634ff
> color (#!3.1 & sel) #ffdd35ff
> color (#!3.1 & sel) #ffe137ff
> color (#!3.1 & sel) #ffee37ff
> color (#!3.1 & sel) #ffef3cff
> color (#!3.1 & sel) #fff047ff
> color (#!3.1 & sel) #ffeb52ff
> color (#!3.1 & sel) #ffdd54ff
> color (#!3.1 & sel) #ffdb57ff
> color (#!3.1 & sel) #ffd558ff
> color (#!3.1 & sel) #ffd15cff
> color (#!3.1 & sel) #ffd15eff
> color (#!3.1 & sel) #ffd75eff
> color (#!3.1 & sel) #ffde65ff
> color (#!3.1 & sel) #ffe167ff
> color (#!3.1 & sel) #ffe26cff
> color (#!3.1 & sel) #ffe874ff
> color (#!3.1 & sel) #ffea7eff
> color (#!3.1 & sel) #ffeb85ff
> color (#!3.1 & sel) #ffe787ff
> color (#!3.1 & sel) #ffe187ff
> color (#!3.1 & sel) #ffd889ff
> color (#!3.1 & sel) #ffd289ff
> color (#!3.1 & sel) #ffca89ff
> color (#!3.1 & sel) #ffc386ff
> color (#!3.1 & sel) #ffbc82ff
> color (#!3.1 & sel) #ffba82ff
> color (#!3.1 & sel) #ffba81ff
> color (#!3.1 & sel) #ffbc81ff
> color (#!3.1 & sel) #ffc081ff
> color (#!3.1 & sel) #ffc481ff
> color (#!3.1 & sel) #ffc97dff
> color (#!3.1 & sel) #ffce79ff
> color (#!3.1 & sel) #ffcc74ff
> color (#!3.1 & sel) #ffcb72ff
> color (#!3.1 & sel) #ffc96bff
> color (#!3.1 & sel) #ffc35cff
> color (#!3.1 & sel) #ffbc49ff
> color (#!3.1 & sel) #ffb73aff
> color (#!3.1 & sel) #ffba2fff
> color (#!3.1 & sel) #ffb829ff
> color (#!3.1 & sel) #ffbd23ff
> color (#!3.1 & sel) #ffb623ff
> select clear
Drag select of 35 residues
> select up
603 atoms, 607 bonds, 75 residues, 2 models selected
> select up
1155 atoms, 1178 bonds, 145 residues, 2 models selected
> color (#!3.4 & sel) dark gray
Drag select of 47 residues
> select clear
Drag select of 61 residues
> select up
882 atoms, 891 bonds, 110 residues, 2 models selected
> color (#!3.1 & sel) dark gray
> select #3.1/Q:2768
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
96 atoms, 98 bonds, 12 residues, 2 models selected
> select up
1159 atoms, 1182 bonds, 145 residues, 2 models selected
> color (#!3.1 & sel) dark gray
> select clear
> show #!3.1-7 surfaces
> hide #!3.1-7 surfaces
Drag select of 63 residues
Drag select of 55 residues
Drag select of 42 residues
Drag select of 47 residues
Drag select of 49 residues
Drag select of 64 residues
Drag select of 50 residues
Drag select of 42 residues
> select up
2077 atoms, 2096 bonds, 257 residues, 4 models selected
> select up
4632 atoms, 4724 bonds, 580 residues, 4 models selected
Drag select of 50 residues
Drag select of 57 residues
Drag select of 52 residues
Drag select of 65 residues
Drag select of 49 residues
> select up
8344 atoms, 8474 bonds, 1039 residues, 8 models selected
> select up
10419 atoms, 10626 bonds, 1305 residues, 8 models selected
> color (#!3.1-2,4,6 & sel) dim gray
> select clear
Drag select of 77 residues
> select up
1031 atoms, 1044 bonds, 129 residues, 2 models selected
Drag select of 7 residues
> select up
1097 atoms, 1114 bonds, 138 residues, 2 models selected
> select down
1086 atoms, 1044 bonds, 136 residues, 2 models selected
> select up
1097 atoms, 1114 bonds, 138 residues, 2 models selected
> select down
1086 atoms, 1044 bonds, 136 residues, 2 models selected
> select clear
Drag select of 81 residues
> select up
974 atoms, 987 bonds, 123 residues, 2 models selected
Drag select of 7 residues
Drag select of 6 residues
> select up
1062 atoms, 1074 bonds, 135 residues, 2 models selected
> select up
1156 atoms, 1176 bonds, 145 residues, 2 models selected
> color (#!3.1 & sel) orange
> select clear
> show #!3.1-7 surfaces
> show #!1 models
> hide #!1 models
> hide #!3.1-7 surfaces
Drag select of 2611 residues
> color sel bychain
> color sel bypolymer
> show sel surfaces
> color sel bypolymer
> hide sel surfaces
> color sel bychain
> show sel surfaces
> hide sel surfaces
> color sel bypolymer
> hide sel surfaces
> show sel surfaces
> show #!1 models
> close #2
> open "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_SNAREpins.pdb"
Summary of feedback from opening C:/Users/grush/Documents/Seminars/Munc13
project/Model_paper/Fig1_SNAREpins.pdb
---
warnings | CONECT record for nonexistent atom: 2613
Start residue of secondary structure not found: HELIX 1 1 VAL A 9 VAL A 21 1
13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
2 messages similar to the above omitted
CONECT record for nonexistent atom: 2613
Start residue of secondary structure not found: HELIX 1 1 VAL A 9 VAL A 21 1
13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
9 messages similar to the above omitted
CONECT record for nonexistent atom: 2613
Start residue of secondary structure not found: HELIX 1 1 VAL A 9 VAL A 21 1
13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
16 messages similar to the above omitted
Chain information for Fig1_SNAREpins.pdb
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A | No description available
2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.6/B | No description available
2.1/C 2.2/C 2.3/C 2.4/C 2.5/C 2.6/C | No description available
2.1/D 2.2/D 2.3/D 2.4/D 2.5/D 2.6/D | No description available
2.1/E 2.2/E 2.3/E 2.4/E 2.5/E 2.6/E | No description available
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel cartoons
> hide #!1 models
> hide #!3 models
Drag select of 11016 atoms
> hide sel atoms
> show sel cartoons
> select clear
> select add #2.4/E:53
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2.5/E:53
10 atoms, 8 bonds, 2 residues, 2 models selected
> select add #2.6/E:53
15 atoms, 12 bonds, 3 residues, 3 models selected
> select add #2.1/E:61
22 atoms, 18 bonds, 4 residues, 4 models selected
> select add #2.2/E:54
27 atoms, 22 bonds, 5 residues, 5 models selected
> select add #2.3/E:60
36 atoms, 30 bonds, 6 residues, 6 models selected
> select up
894 atoms, 894 bonds, 114 residues, 6 models selected
> color sel cyan
> select clear
> select #2.4/B:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2.3/B:240
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #2.5/B:193
18 atoms, 15 bonds, 3 residues, 3 models selected
> select add #2.2/B:240
23 atoms, 19 bonds, 4 residues, 4 models selected
> select add #2.1/B:240
28 atoms, 23 bonds, 5 residues, 5 models selected
> select add #2.6/B:240
33 atoms, 27 bonds, 6 residues, 6 models selected
> select up
2496 atoms, 2520 bonds, 306 residues, 6 models selected
> select up
2598 atoms, 2622 bonds, 324 residues, 6 models selected
> color sel blue
> select clear
> select add #2.5/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2.4/A:33
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add #2.3/A:33
27 atoms, 24 bonds, 3 residues, 3 models selected
> select add #2.2/A:61
33 atoms, 29 bonds, 4 residues, 4 models selected
> select add #2.1/A:60
41 atoms, 36 bonds, 5 residues, 5 models selected
> select add #2.6/A:58
50 atoms, 44 bonds, 6 residues, 6 models selected
> select up
1740 atoms, 1734 bonds, 210 residues, 6 models selected
> select up
1884 atoms, 1878 bonds, 228 residues, 6 models selected
> color sel red
> color sel blue
> select #2.5/B:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2.6/B:201
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #2.4/B:196
25 atoms, 22 bonds, 3 residues, 3 models selected
> select add #2.3/B:240
30 atoms, 26 bonds, 4 residues, 4 models selected
> select add #2.2/B:193
36 atoms, 31 bonds, 5 residues, 5 models selected
> select add #2.1/B:240
41 atoms, 35 bonds, 6 residues, 6 models selected
> select up
2496 atoms, 2520 bonds, 306 residues, 6 models selected
> select up
2598 atoms, 2622 bonds, 324 residues, 6 models selected
> color sel red
> select clear
> select #2.4/D:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2.5/D:179
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #2.6/D:173
24 atoms, 21 bonds, 3 residues, 3 models selected
> select add #2.1/C:35
32 atoms, 28 bonds, 4 residues, 4 models selected
> select clear
> select #2.4/D:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2.5/D:172
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #2.6/D:172
24 atoms, 21 bonds, 3 residues, 3 models selected
> select add #2.1/D:172
32 atoms, 28 bonds, 4 residues, 4 models selected
> select add #2.2/D:179
40 atoms, 35 bonds, 5 residues, 5 models selected
> select add #2.3/D:176
51 atoms, 45 bonds, 6 residues, 6 models selected
> select up
2382 atoms, 2382 bonds, 318 residues, 6 models selected
> select up
2442 atoms, 2442 bonds, 330 residues, 6 models selected
> color sel forest green
> select clear
> select #2.3/C:17
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2.2/C:19
19 atoms, 17 bonds, 2 residues, 2 models selected
> select add #2.1/C:15
28 atoms, 25 bonds, 3 residues, 3 models selected
> select add #2.6/C:15
37 atoms, 33 bonds, 4 residues, 4 models selected
> select add #2.5/C:17
48 atoms, 43 bonds, 5 residues, 5 models selected
> select add #2.4/C:16
53 atoms, 47 bonds, 6 residues, 6 models selected
> select up
2802 atoms, 2802 bonds, 360 residues, 6 models selected
> select up
2976 atoms, 2976 bonds, 390 residues, 6 models selected
> color sel lime
> select clear
> select add #2.3/E:55
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2.2/E:54
13 atoms, 11 bonds, 2 residues, 2 models selected
> select add #2.1/E:54
18 atoms, 15 bonds, 3 residues, 3 models selected
> select add #2.4/E:53
23 atoms, 19 bonds, 4 residues, 4 models selected
> select add #2.6/E:54
28 atoms, 23 bonds, 5 residues, 5 models selected
> select up
745 atoms, 745 bonds, 95 residues, 5 models selected
> select up
925 atoms, 925 bonds, 125 residues, 5 models selected
> select add #2.5/E:54
930 atoms, 929 bonds, 126 residues, 6 models selected
> select up
1074 atoms, 1074 bonds, 144 residues, 6 models selected
> select up
1110 atoms, 1110 bonds, 150 residues, 6 models selected
> color sel cyan
> select clear
> show #2.1-6 surfaces
> hide #!2.1-6 surfaces
> show #!2.1-6 surfaces
> hide #!2.1-6 surfaces
Drag select of 1422 residues
> select clear
Drag select of 1422 residues
> show sel surfaces
> hide sel surfaces
> select clear
> select add #2.4/E:53
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2.3/E:57
10 atoms, 8 bonds, 2 residues, 3 models selected
> select add #2.2/E:54
15 atoms, 12 bonds, 3 residues, 5 models selected
> select add #2.5/E:63
26 atoms, 22 bonds, 4 residues, 7 models selected
> select add #2.6/E:61
33 atoms, 28 bonds, 5 residues, 9 models selected
> select add #2.1/E:57
38 atoms, 32 bonds, 6 residues, 11 models selected
> select up
894 atoms, 894 bonds, 114 residues, 12 models selected
> select up
1110 atoms, 1110 bonds, 150 residues, 12 models selected
> color (#!2.1-6 & sel) cyan
> select clear
> select #2.2/B:240
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2.3/B:240
10 atoms, 8 bonds, 2 residues, 3 models selected
> select add #2.4/B:240
15 atoms, 12 bonds, 3 residues, 5 models selected
> select add #2.5/B:237
22 atoms, 18 bonds, 4 residues, 7 models selected
> select add #2.6/B:193
28 atoms, 23 bonds, 5 residues, 9 models selected
> select add #2.1/B:240
33 atoms, 27 bonds, 6 residues, 11 models selected
> select up
2496 atoms, 2520 bonds, 306 residues, 12 models selected
> select up
2598 atoms, 2622 bonds, 324 residues, 12 models selected
> color (#!2.1-6 & sel) red
> select clear
> select add #2.2/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2.1/A:62
18 atoms, 16 bonds, 2 residues, 3 models selected
> select add #2.6/A:58
27 atoms, 24 bonds, 3 residues, 5 models selected
> select add #2.5/A:60
35 atoms, 31 bonds, 4 residues, 7 models selected
> select add #2.4/A:55
44 atoms, 39 bonds, 5 residues, 9 models selected
> select add #2.3/A:55
53 atoms, 47 bonds, 6 residues, 11 models selected
> select up
1740 atoms, 1734 bonds, 210 residues, 12 models selected
> select up
1884 atoms, 1878 bonds, 228 residues, 12 models selected
> color (#!2.1-6 & sel) blue
> select clear
> select #2.3/D:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2.2/D:194
18 atoms, 16 bonds, 2 residues, 3 models selected
> select add #2.1/D:190
25 atoms, 22 bonds, 3 residues, 5 models selected
> select add #2.6/C:65
33 atoms, 29 bonds, 4 residues, 7 models selected
> select add #2.5/D:183
38 atoms, 33 bonds, 5 residues, 9 models selected
> select add #2.4/D:190
45 atoms, 39 bonds, 6 residues, 11 models selected
> select up
2452 atoms, 2452 bonds, 325 residues, 12 models selected
> select up
2531 atoms, 2531 bonds, 340 residues, 12 models selected
> color (#!2.1-6 & sel) forest green
> select clear
> select #2.3/C:72
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2.4/C:71
13 atoms, 11 bonds, 2 residues, 3 models selected
> select add #2.5/C:72
18 atoms, 15 bonds, 3 residues, 5 models selected
> select add #2.1/C:24
27 atoms, 23 bonds, 4 residues, 7 models selected
> select add #2.2/C:15
36 atoms, 31 bonds, 5 residues, 9 models selected
> select add #2.3/C:17
47 atoms, 41 bonds, 6 residues, 10 models selected
> select add #2.6/C:17
58 atoms, 51 bonds, 7 residues, 11 models selected
> select up
2802 atoms, 2802 bonds, 360 residues, 12 models selected
> select up
2976 atoms, 2976 bonds, 390 residues, 12 models selected
> color (#!2.1-6 & sel) lime
> select clear
[Repeated 2 time(s)]
> select #2.6/D:179
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
397 atoms, 397 bonds, 53 residues, 2 models selected
> select up
407 atoms, 407 bonds, 55 residues, 2 models selected
> color (#!2.6 & sel) forest green
> select clear
> show #!2.1-6 surfaces
> show #!1 models
> show #!3 models
> save "C:/Users/grush/Documents/Seminars/Munc13 project/Model_paper/Fig1.cxs"
> open "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_Syp+Vamp.pdb"
Summary of feedback from opening C:/Users/grush/Documents/Seminars/Munc13
project/Model_paper/Fig1_Syp+Vamp.pdb
---
warnings | CONECT record for nonexistent atom: 2613
CONECT record for nonexistent atom: 2614
CONECT record for nonexistent atom: 2657
CONECT record for nonexistent atom: 3163
CONECT record for nonexistent atom: 3184
72 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 VAL A 9 VAL A 21 1
13
Start residue of secondary structure not found: HELIX 2 2 GLU A 24 CYS A 44 1
21
Start residue of secondary structure not found: HELIX 3 3 PRO A 85 THR A 91 1
7
Start residue of secondary structure not found: HELIX 4 4 ALA A 104 TYR A 132
1 29
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 SER A 156
1 21
72 messages similar to the above omitted
Fig1_Syp+Vamp.pdb title:
EM density fit model of syp/syb complex [more info...]
Chain information for Fig1_Syp+Vamp.pdb
---
Chain | Description
4.1/A 4.2/B 4.3/C 4.4/D 4.5/E 4.6/F | No description available
4.7/X 4.8/X 4.9/X 4.10/X 4.11/X 4.12/X | No description available
Drag select of 1177 residues
> select up
12198 atoms, 12390 bonds, 1393 residues, 12 models selected
> select up
25128 atoms, 25608 bonds, 2574 residues, 12 models selected
> show sel surfaces
> hide sel surfaces
> select clear
Drag select of 295 residues
> select up
4523 atoms, 4575 bonds, 594 residues, 12 models selected
> select up
14256 atoms, 14646 bonds, 1878 residues, 12 models selected
> color (#!4.1-6 & sel) purple
> select clear
> select #4.8/X:103
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #4.9/X:86
35 atoms, 33 bonds, 2 residues, 3 models selected
> select add #4.11/X:83
57 atoms, 54 bonds, 3 residues, 5 models selected
> select add #4.10/X:105
76 atoms, 72 bonds, 4 residues, 7 models selected
> select add #4.12/X:99
95 atoms, 90 bonds, 5 residues, 9 models selected
> select add #4.7/X:113
116 atoms, 111 bonds, 6 residues, 11 models selected
> select up
2204 atoms, 2210 bonds, 128 residues, 12 models selected
> select up
10872 atoms, 10962 bonds, 696 residues, 12 models selected
> color (#!4.7-12 & sel) blue
> select clear
> hide #!2 models
> hide #!1.1-6#!3.1-7#!4.1-12 surfaces
> show #!1.1-6#!3.1-7#!4.1-12 surfaces
> save "C:/Users/grush/Documents/Seminars/Munc13 project/Model_paper/Fig1.cxs"
——— End of log from Wed Mar 29 12:26:29 2023 ———
opened ChimeraX session
> select #1.6/B:1191@CG
1 atom, 1 residue, 1 model selected
> select add #1.2/B:1191@OE1
2 atoms, 2 residues, 3 models selected
> select add #1.5/B:974@OE2
3 atoms, 3 residues, 5 models selected
> select add #1.4/B:1190@O
4 atoms, 4 residues, 7 models selected
> select add #1.3/B:1127@CB
5 atoms, 5 residues, 9 models selected
> select add #1.6
9548 atoms, 9648 bonds, 9 pseudobonds, 598 residues, 11 models selected
> select subtract #1.6
4 atoms, 4 residues, 9 models selected
> select add #1.6
9548 atoms, 9648 bonds, 9 pseudobonds, 598 residues, 10 models selected
> select add #1.5
19091 atoms, 19296 bonds, 18 pseudobonds, 1191 residues, 12 models selected
> select subtract #1.5
9547 atoms, 9648 bonds, 9 pseudobonds, 597 residues, 10 models selected
> select add #1.5
19091 atoms, 19296 bonds, 18 pseudobonds, 1191 residues, 11 models selected
> select add #1.4
28634 atoms, 28944 bonds, 27 pseudobonds, 1784 residues, 13 models selected
> select subtract #1.4
19090 atoms, 19296 bonds, 18 pseudobonds, 1190 residues, 11 models selected
> select add #1.4
28634 atoms, 28944 bonds, 27 pseudobonds, 1784 residues, 12 models selected
> select add #1.3
38177 atoms, 38592 bonds, 36 pseudobonds, 2377 residues, 14 models selected
> select add #1.1
47721 atoms, 48240 bonds, 45 pseudobonds, 2971 residues, 16 models selected
> select add #1
57264 atoms, 57888 bonds, 54 pseudobonds, 3564 residues, 19 models selected
> hide sel surfaces
> color (#!1.1-6 & sel) gray
> show sel surfaces
> select clear
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!2 models
> save "C:/Users/grush/Documents/Seminars/Munc13 project/Model_paper/Fig1.cxs"
——— End of log from Fri Apr 21 11:53:23 2023 ———
opened ChimeraX session
> hide #!1 models
> hide #!2.1-6#!3.1-7 surfaces
> open "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Syt_ring_p_cSNAREs.pdb"
Summary of feedback from opening C:/Users/grush/Documents/Seminars/Munc13
project/Model_paper/Syt_ring_p_cSNAREs.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 30
ASP A 64 1 35
Start residue of secondary structure not found: HELIX 2 2 LEU B 192 ASP B 242
1 51
Start residue of secondary structure not found: HELIX 3 3 LEU C 11 GLU C 73 1
63
Start residue of secondary structure not found: HELIX 4 4 ARG D 142 GLU D 194
1 53
Start residue of secondary structure not found: HELIX 5 5 TYR E 52 TYR E 70 1
19
36 messages similar to the above omitted
Chain information for Syt_ring_p_cSNAREs.pdb
---
Chain | Description
5.8/A 5.9/A 5.10/A 5.11/A 5.12/A 5.13/A | No description available
5.8/B 5.9/B 5.10/B 5.11/B 5.12/B 5.13/B | No description available
5.8/C 5.9/C 5.10/C 5.11/C 5.12/C 5.13/C | No description available
5.8/D 5.9/D 5.10/D 5.11/D 5.12/D 5.13/D | No description available
5.2/F 5.3/F 5.4/F 5.5/F 5.6/F 5.7/F | No description available
5.1/G | No description available
5.8/I 5.9/I 5.10/I 5.11/I 5.12/I 5.13/I | No description available
5.8/J 5.9/J 5.10/J 5.11/J 5.12/J 5.13/J | No description available
5.8/K 5.9/K 5.10/K 5.11/K 5.12/K 5.13/K | No description available
5.8/L 5.9/L 5.10/L 5.11/L 5.12/L 5.13/L | No description available
5.1/Q | No description available
5.8/n 5.9/n 5.10/n 5.11/n 5.12/n 5.13/n | No description available
> show #5.2-13#!2.1-6#!3.1-7#!5.1 cartoons
> hide #5.2-13#!2.1-6#!3.1-7#!5.1 atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #5.13/B:210
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
416 atoms, 420 bonds, 51 residues, 1 model selected
> select up
433 atoms, 437 bonds, 54 residues, 1 model selected
> color sel red
> select #5.13/A:50
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel blue
> select up
290 atoms, 289 bonds, 35 residues, 1 model selected
> select up
314 atoms, 313 bonds, 38 residues, 1 model selected
> color sel blue
> select #5.13/C:45
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
486 atoms, 486 bonds, 63 residues, 1 model selected
> select up
496 atoms, 496 bonds, 65 residues, 1 model selected
> color sel blue
> color sel lime
> select #5.13/D:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
397 atoms, 397 bonds, 53 residues, 1 model selected
> select up
407 atoms, 407 bonds, 55 residues, 1 model selected
> color sel forest green
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
[Repeated 1 time(s)]
> select #5.13/n:68
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
369 atoms, 371 bonds, 45 residues, 1 model selected
> select up
3859 atoms, 3868 bonds, 485 residues, 1 model selected
> select down
369 atoms, 371 bonds, 45 residues, 1 model selected
> color sel cyan
> select clear
> hide #!3 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #5.7 models
> show #5.7 models
> close #5.2-7#5.1
Drag select of 2910 residues
> show sel surfaces
> hide sel surfaces
> select clear
> select #5.13/I:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
278 atoms, 277 bonds, 34 residues, 2 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 2 models selected
> select down
278 atoms, 277 bonds, 34 residues, 10 models selected
> color (#!5.13 & sel) blue
> select #5.13/J:194
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
481 atoms, 486 bonds, 59 residues, 2 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 2 models selected
> select down
481 atoms, 486 bonds, 59 residues, 10 models selected
> color (#!5.13 & sel) red
> select clear
[Repeated 3 time(s)]Drag select of 6 residues
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> color (#!5.13 & sel) lime
Drag select of 2 residues
> select up
505 atoms, 505 bonds, 64 residues, 2 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 2 models selected
> select down
505 atoms, 505 bonds, 64 residues, 10 models selected
> color (#!5.13 & sel) forest green
> select clear
> select #5.8/n:50
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #5.12/n:50
10 atoms, 8 bonds, 2 residues, 3 models selected
> select add #5.9/n:50
15 atoms, 12 bonds, 3 residues, 5 models selected
> select add #5.10/n:47
24 atoms, 20 bonds, 4 residues, 7 models selected
> select add #5.11/n:50
29 atoms, 24 bonds, 5 residues, 9 models selected
> select up
1845 atoms, 1855 bonds, 225 residues, 10 models selected
> color (#!5.8-12 & sel) cyan
> select clear
[Repeated 2 time(s)]Drag select of 16 residues
> select up
278 atoms, 277 bonds, 34 residues, 2 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 2 models selected
> select down
278 atoms, 277 bonds, 34 residues, 10 models selected
> color (#!5.8 & sel) blue
> select clear
Drag select of 3 residues
> select up
481 atoms, 486 bonds, 59 residues, 2 models selected
> color (#!5.8 & sel) red
> select clear
Drag select of 15 residues
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> color (#!5.8 & sel) lime
Drag select of 10 residues
> select up
505 atoms, 505 bonds, 64 residues, 2 models selected
> color (#!5.8 & sel) forest green
> select clear
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> select #5.9/I:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
278 atoms, 277 bonds, 34 residues, 2 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 2 models selected
> select down
278 atoms, 277 bonds, 34 residues, 10 models selected
> color (#!5.9 & sel) blue
Drag select of 3 residues
> select up
481 atoms, 486 bonds, 59 residues, 2 models selected
> color (#!5.9 & sel) red
Drag select of 5 residues
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> color (#!5.9 & sel) lime
Drag select of 6 residues
> select up
505 atoms, 505 bonds, 64 residues, 2 models selected
> color (#!5.9 & sel) forest green
> select clear
Drag select of 1 residues
> select up
278 atoms, 277 bonds, 34 residues, 2 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 2 models selected
> select down
278 atoms, 277 bonds, 34 residues, 10 models selected
> color (#!5.10 & sel) blue
> select clear
Drag select of 2 residues
> select up
481 atoms, 486 bonds, 59 residues, 2 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 2 models selected
> select down
481 atoms, 486 bonds, 59 residues, 10 models selected
> color (#!5.10 & sel) red
> select clear
Drag select of 5 residues
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> color (#!5.10 & sel) lime
Drag select of 3 residues
> select up
505 atoms, 505 bonds, 64 residues, 2 models selected
> color (#!5.10 & sel) forest green
> select clear
Drag select of 3 residues
> select up
278 atoms, 277 bonds, 34 residues, 2 models selected
> color (#!5.11 & sel) blue
Drag select of 2 residues
> select up
481 atoms, 486 bonds, 59 residues, 2 models selected
> color (#!5.11 & sel) red
Drag select of 6 residues
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> color (#!5.11 & sel) lime
Drag select of 2 residues
> select up
505 atoms, 505 bonds, 64 residues, 2 models selected
> color (#!5.11 & sel) forest green
> select clear
[Repeated 1 time(s)]Drag select of 1 residues
> select up
278 atoms, 277 bonds, 34 residues, 2 models selected
> color (#!5.12 & sel) blue
Drag select of 3 residues
> select up
481 atoms, 486 bonds, 59 residues, 2 models selected
> color (#!5.12 & sel) red
Drag select of 2 residues
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> color (#!5.12 & sel) lime
Drag select of 3 residues
> select up
505 atoms, 505 bonds, 64 residues, 2 models selected
> color (#!5.12 & sel) forest green
> select clear
Drag select of 64 residues
> select up
1607 atoms, 1610 bonds, 205 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> delete sel
Drag select of 62 residues
> select up
1612 atoms, 1615 bonds, 206 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> delete sel
Drag select of 58 residues
> select up
1612 atoms, 1615 bonds, 206 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> delete sel
Drag select of 67 residues
> select up
1612 atoms, 1615 bonds, 206 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> delete sel
Drag select of 66 residues
> select up
1612 atoms, 1615 bonds, 206 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> delete sel
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!2 models
> select clear
> select #2.4/E:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
31 atoms, 30 bonds, 5 residues, 2 models selected
> select up
185 atoms, 185 bonds, 25 residues, 2 models selected
> delete sel
Drag select of 4 residues
> select up
31 atoms, 30 bonds, 5 residues, 2 models selected
> select up
185 atoms, 185 bonds, 25 residues, 2 models selected
> delete sel
Drag select of 3 residues
> select up
31 atoms, 30 bonds, 5 residues, 2 models selected
> select up
185 atoms, 185 bonds, 25 residues, 2 models selected
> delete sel
Drag select of 2 residues
> select up
31 atoms, 30 bonds, 5 residues, 2 models selected
> select up
185 atoms, 185 bonds, 25 residues, 2 models selected
> delete sel
Drag select of 3 residues
> select up
31 atoms, 30 bonds, 5 residues, 2 models selected
> select up
185 atoms, 185 bonds, 25 residues, 2 models selected
> delete sel
> save "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_with_peripherals.cxs"
——— End of log from Sat Jun 24 02:02:49 2023 ———
opened ChimeraX session
> ui tool show "Side View"
> show #!4 models
> hide #!4 models
> show #!2.1-6#!3.1-7#!5.8-13 surfaces
> select #5.12/K:38@CD
1 atom, 1 residue, 1 model selected
> select #5.12/K:41@OD2
1 atom, 1 residue, 1 model selected
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 7 models selected
> select subtract #5
34 models selected
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 7 models selected
> select subtract #5
34 models selected
> hide #!5 models
> show #!5 models
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 7 models selected
> transparency (#!5.8-13 & sel) 60
> transparency (#!5.8-13 & sel) 70
> select clear
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 7 models selected
> transparency (#!5.8-13 & sel) 50
> select clear
> hide #!5 models
> show #!5 models
> hide #!2.1-6#!3.1-7#!5.8-13 cartoons
[Repeated 1 time(s)]
> show #!2.1-6#!3.1-7#!5.8-13 cartoons
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 7 models selected
> graphics silhouettes true
> graphics silhouettes false
> hide #!2 models
> show #!2 models
> hide #!2 models
> graphics silhouettes true
> show #!2 models
> graphics silhouettes false
> help help:quickstart
[Repeated 1 time(s)]
> graphics silhouettes true
> ui tool show "Selection Inspector"
> select #3.1/G:2319@CB
1 atom, 1 residue, 1 model selected
> select #3.1/G:2330@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
77 atoms, 76 bonds, 10 residues, 2 models selected
> select up
1159 atoms, 1182 bonds, 145 residues, 2 models selected
> select up
1168 atoms, 1189 bonds, 147 residues, 2 models selected
> select up
3477 atoms, 3546 bonds, 435 residues, 2 models selected
> select down
1168 atoms, 1189 bonds, 147 residues, 2 models selected
> select #3.1/Q:3010@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
77 atoms, 76 bonds, 10 residues, 2 models selected
> select up
1159 atoms, 1182 bonds, 145 residues, 2 models selected
> ui tool show "Selection Inspector"
> graphics silhouettes false
> graphics silhouettes true
> select add #5
16063 atoms, 16125 bonds, 1995 residues, 9 models selected
> select add #3.1
28820 atoms, 29135 bonds, 5 pseudobonds, 3591 residues, 44 models selected
> select subtract #3.1
14904 atoms, 14943 bonds, 1850 residues, 43 models selected
> view #5 clip false
> set silhouetteWidth 4
> set silhouetteWidth 2
> select clear
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 7 models selected
> select subtract #5
34 models selected
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 7 models selected
> transparency (#!5.8-13 & sel) 90
> hide sel cartoons
> select clear
> select add #2
10091 atoms, 10103 bonds, 1303 residues, 7 models selected
> select add #3
30937 atoms, 31363 bonds, 5 pseudobonds, 3914 residues, 41 models selected
> select #5.12/K:34@CD
1 atom, 1 residue, 1 model selected
> select #5.12/K:30@NH1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> select up
2209 atoms, 2215 bonds, 273 residues, 2 models selected
> transparency (#!5.12 & sel) 0
> select clear
> select add #3
20846 atoms, 21260 bonds, 5 pseudobonds, 2611 residues, 9 models selected
> select add #2
30937 atoms, 31363 bonds, 5 pseudobonds, 3914 residues, 24 models selected
> show sel cartoons
> select add #5
45841 atoms, 46306 bonds, 5 pseudobonds, 5764 residues, 56 models selected
> show sel cartoons
> hide sel cartoons
> select clear
> select add #4.1
2376 atoms, 2441 bonds, 313 residues, 1 model selected
> select add #4.2
4752 atoms, 4882 bonds, 626 residues, 3 models selected
> select add #4.3
7128 atoms, 7323 bonds, 939 residues, 5 models selected
> select add #4.4
9504 atoms, 9764 bonds, 1252 residues, 7 models selected
> select add #4.5
11880 atoms, 12205 bonds, 1565 residues, 9 models selected
> select add #4.6
14256 atoms, 14646 bonds, 1878 residues, 11 models selected
> hide #!4.11 models
> hide #!4.10 models
> hide #!4.9 models
> hide #!4.8 models
> hide #!4.7 models
> show #!4 models
> hide #!4.6 models
> show #!4.6 models
> hide #!4.12 models
> select add #3.7
15411 atoms, 15824 bonds, 2023 residues, 13 models selected
> select subtract #3.7
14256 atoms, 14646 bonds, 1878 residues, 13 models selected
> select add #3
35102 atoms, 35906 bonds, 5 pseudobonds, 4489 residues, 21 models selected
> select add #2
45193 atoms, 46009 bonds, 5 pseudobonds, 5792 residues, 36 models selected
> save "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_with_peripherals.cxs"
——— End of log from Wed Jun 28 13:03:52 2023 ———
opened ChimeraX session
> open C:/Users/grush/Dropbox/Chimera/PDB/SybAFold_sym6.PDB
Summary of feedback from opening
C:/Users/grush/Dropbox/Chimera/PDB/SybAFold_sym6.PDB
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 2
GLY A 16 1 15
Start residue of secondary structure not found: HELIX 2 2 PHE A 19 LYS A 23 1
5
Start residue of secondary structure not found: HELIX 3 3 PRO A 25 GLY A 45 1
21
Start residue of secondary structure not found: HELIX 4 4 LYS A 60 GLU A 62 1
3
Start residue of secondary structure not found: HELIX 5 5 LEU A 77 GLN A 79 1
3
10 messages similar to the above omitted
SybAFold_sym6.PDB title:
Alphafold monomer V2.0 prediction for synaptophysin (P08247) [more info...]
Chain information for SybAFold_sym6.PDB
---
Chain | Description | UniProt
6.1/A | synaptophysin | SYPH_HUMAN 1-313
6.2/A 6.3/A 6.4/A 6.5/A 6.6/A | synaptophysin | SYPH_HUMAN 1-313
> select add #2
45193 atoms, 46009 bonds, 5 pseudobonds, 5792 residues, 21 models selected
> select add #2
45193 atoms, 46009 bonds, 5 pseudobonds, 5792 residues, 21 models selected
> select add #2
45193 atoms, 46009 bonds, 5 pseudobonds, 5792 residues, 21 models selected
> select add #2
45193 atoms, 46009 bonds, 5 pseudobonds, 5792 residues, 21 models selected
> select add #2
45193 atoms, 46009 bonds, 5 pseudobonds, 5792 residues, 21 models selected
> select add #1
102457 atoms, 103897 bonds, 59 pseudobonds, 9356 residues, 34 models selected
> select subtract #1
45193 atoms, 46009 bonds, 5 pseudobonds, 5792 residues, 27 models selected
> select clear
[Repeated 1 time(s)]
> select add #6
10993 atoms, 11286 bonds, 1399 residues, 8 models selected
> view matrix models
> #6,0.62402,0.40474,0.66841,18.509,-0.76376,0.13517,0.63119,-35.753,0.16512,-0.90439,0.39347,-40.062
> view matrix models
> #6,0.60321,0.40824,0.68519,18.587,-0.78646,0.16145,0.59617,-34.591,0.13275,-0.89849,0.41845,-39.751
> ui mousemode right "move picked models"
> select clear
[Repeated 4 time(s)]
> select #6.7/?:1@He1
1 atom, 1 residue, 1 model selected
> select #6.7/?:1@He1
1 atom, 1 residue, 1 model selected
> delete sel
> select add #6
10992 atoms, 11286 bonds, 1398 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.60321,0.40824,0.68519,18.658,-0.78646,0.16145,0.59617,-22.243,0.13275,-0.89849,0.41845,-107.47
> select #4.5/E:81@O
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
321 atoms, 327 bonds, 40 residues, 2 models selected
> select add #4
25128 atoms, 25608 bonds, 2574 residues, 14 models selected
> show sel & #!4.1-6 surfaces
> hide sel & #!4.1-6 surfaces
> select clear
> select add #6
10992 atoms, 11286 bonds, 1398 residues, 7 models selected
> view matrix models
> #6,0.60321,0.40824,0.68519,16.587,-0.78646,0.16145,0.59617,-22.482,0.13275,-0.89849,0.41845,-104.08
> view matrix models
> #6,0.60321,0.40824,0.68519,19.109,-0.78646,0.16145,0.59617,-26.693,0.13275,-0.89849,0.41845,-101.24
> view matrix models
> #6,0.60321,0.40824,0.68519,18.379,-0.78646,0.16145,0.59617,-25.941,0.13275,-0.89849,0.41845,-104.71
> select subtract #6
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select #6.5/A:43
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
164 atoms, 170 bonds, 21 residues, 1 model selected
> select up
1832 atoms, 1881 bonds, 233 residues, 1 model selected
> select up
10992 atoms, 11286 bonds, 1398 residues, 6 models selected
> select up
10992 atoms, 11286 bonds, 1398 residues, 7 models selected
> select down
10992 atoms, 11286 bonds, 1398 residues, 6 models selected
> color sel dark gray
> select clear
[Repeated 1 time(s)]
> close #4
> select add #6
10992 atoms, 11286 bonds, 1398 residues, 7 models selected
> view matrix models
> #6,0.60321,0.40824,0.68519,14.382,-0.78646,0.16145,0.59617,-24.518,0.13275,-0.89849,0.41845,-107.58
[Repeated 1 time(s)]
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.65367,0.2532,0.71316,7.4202,-0.7565,0.19325,0.62478,-23.05,0.020373,-0.94791,0.31787,-109.93
> view matrix models
> #6,0.67545,0.25919,0.69035,7.6911,-0.73628,0.18546,0.65076,-23.373,0.040638,-0.94785,0.31611,-109.91
> view matrix models
> #6,0.66297,0.25437,0.70411,7.4659,-0.74599,0.14528,0.64992,-25.183,0.063028,-0.95613,0.28607,-110.27
> ui tool show "Side View"
> select clear
> select add #6
10992 atoms, 11286 bonds, 1398 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.66297,0.25437,0.70411,7.3097,-0.74599,0.14528,0.64992,-26.034,0.063028,-0.95613,0.28607,-103.73
> view matrix models
> #6,0.66297,0.25437,0.70411,7.4234,-0.74599,0.14528,0.64992,-26.151,0.063028,-0.95613,0.28607,-102.91
> select clear
> select add #6
10992 atoms, 11286 bonds, 1398 residues, 7 models selected
> show sel surfaces
> select clear
> hide #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> show #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> hide #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> select clear
[Repeated 1 time(s)]Drag select of 17 residues
> delete sel
> select clear
Drag select of 17 residues
> delete sel
> select clear
Drag select of 16 residues
> delete sel
Drag select of 17 residues
> delete sel
Drag select of 17 residues
> delete sel
Drag select of 17 residues
> delete sel
> show #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> select #5.11/J:203@CD1
1 atom, 1 residue, 1 model selected
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 8 models selected
> transparency (#!5.8-13 & sel) 0
> select clear
> lighting full
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting full
> lighting direction 1,1,-1
> lighting direction 1,6,-1
> lighting direction 1,-6,-1
> lighting direction 1,-1,-1
> lighting direction 0.577,-0.577,-0.577
> select add #6
10276 atoms, 10570 bonds, 1297 residues, 7 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.66472,0.23703,0.7085,6.6669,-0.72145,-0.042685,0.69115,-34.283,0.19407,-0.97056,0.14263,-104.26
> view matrix models
> #6,0.66034,0.25469,0.70646,7.4305,-0.74713,0.12788,0.65225,-26.962,0.075775,-0.95853,0.27473,-103.07
> view matrix models
> #6,0.66873,0.25636,0.69791,7.4608,-0.74051,0.1455,0.6561,-26.203,0.066653,-0.95557,0.28714,-102.89
> view matrix models
> #6,0.6181,0.43467,0.65499,15.283,-0.76021,0.11844,0.63879,-27.373,0.20009,-0.89277,0.40365,-100.23
> view matrix models
> #6,0.59984,0.48098,0.63941,17.318,-0.76489,0.1102,0.63467,-27.732,0.2348,-0.86978,0.434,-99.237
> view matrix models
> #6,0.60622,0.48091,0.63342,17.274,-0.76904,0.15148,0.621,-25.942,0.20269,-0.86358,0.46167,-98.772
> view matrix models
> #6,0.59269,0.48034,0.64653,17.312,-0.77908,0.13823,0.6115,-26.522,0.20436,-0.86612,0.45615,-98.9
> view matrix models
> #6,0.56712,0.48007,0.66926,17.415,-0.80005,0.12802,0.58612,-26.983,0.1957,-0.86784,0.45668,-98.954
> save "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_with_peripherals_colors.cxs"
——— End of log from Wed Jun 28 14:44:32 2023 ———
opened ChimeraX session
> select add #2
20367 atoms, 20673 bonds, 2600 residues, 13 models selected
> select add #5
35271 atoms, 35616 bonds, 4450 residues, 45 models selected
> select subtract #5
20367 atoms, 20673 bonds, 2600 residues, 72 models selected
> select subtract #2
10276 atoms, 10570 bonds, 1297 residues, 31 models selected
> graphics silhouettes true
> select clear
> select add #2
10091 atoms, 10103 bonds, 1303 residues, 7 models selected
> select add #5
24995 atoms, 25046 bonds, 3153 residues, 39 models selected
> select subtract #2.1
23344 atoms, 23393 bonds, 2940 residues, 72 models selected
> select subtract #5.12
21135 atoms, 21178 bonds, 2667 residues, 67 models selected
> transparency (#!2.2-6#!5.8-11,13 & sel) 80
> select clear
> select add #2.1
1651 atoms, 1653 bonds, 213 residues, 1 model selected
> select add #5.12
3860 atoms, 3868 bonds, 486 residues, 6 models selected
> select add #3
24706 atoms, 25128 bonds, 5 pseudobonds, 3097 residues, 20 models selected
> select add #6
34982 atoms, 35698 bonds, 5 pseudobonds, 4394 residues, 35 models selected
> select subtract #3.3
33827 atoms, 34520 bonds, 5 pseudobonds, 4249 residues, 40 models selected
> select add #2
42267 atoms, 42970 bonds, 5 pseudobonds, 5339 residues, 45 models selected
> select subtract #2
32176 atoms, 32867 bonds, 5 pseudobonds, 4036 residues, 59 models selected
> select add #3
33331 atoms, 34045 bonds, 5 pseudobonds, 4181 residues, 35 models selected
> select subtract #3
12485 atoms, 12785 bonds, 1570 residues, 27 models selected
> select add #5
25180 atoms, 25513 bonds, 3147 residues, 25 models selected
> select subtract #5
10276 atoms, 10570 bonds, 1297 residues, 47 models selected
> select subtract #6
6 models selected
> select add #5.11
2209 atoms, 2215 bonds, 273 residues, 1 model selected
> color (#!5.11 & sel) #b0fbffff
> color (#!5.11 & sel) #acfeffff
> color (#!5.11 & sel) #78ffb5ff
> color (#!5.11 & sel) #77ffb4ff
> color (#!5.11 & sel) #6cff8eff
> color (#!5.11 & sel) #6bff84ff
> color (#!5.11 & sel) #6cff89ff
> color (#!5.11 & sel) #6fff93ff
> color (#!5.11 & sel) #73ffa2ff
> color (#!5.11 & sel) #73ffa6ff
> color (#!5.11 & sel) #72ffa6ff
> color (#!5.11 & sel) #70ff9dff
> color (#!5.11 & sel) #6cff8eff
> color (#!5.11 & sel) #6aff83ff
> color (#!5.11 & sel) #67ff79ff
> color (#!5.11 & sel) #66ff73ff
> color (#!5.11 & sel) #66ff70ff
> color (#!5.11 & sel) #63ff63ff
> color (#!5.11 & sel) #62ff62ff
> color (#!5.11 & sel) #63ff63ff
> color (#!5.11 & sel) #65ff65ff
> color (#!5.11 & sel) #69ff75ff
> color (#!5.11 & sel) #6bff7cff
> color (#!5.11 & sel) #6cff7dff
> color (#!5.11 & sel) #67ff7eff
> color (#!5.11 & sel) #67ff80ff
> color (#!5.11 & sel) #67ff8dff
> color (#!5.11 & sel) #67ff92ff
> color (#!5.11 & sel) #67ff8dff
> color (#!5.11 & sel) #66ff8aff
> color (#!5.11 & sel) #65ff84ff
> color (#!5.11 & sel) #65ff7fff
> transparency (#!5.11 & sel) 80
> transparency (#!5.11 & sel) 60
> select clear
> select add #2.2
1651 atoms, 1653 bonds, 213 residues, 1 model selected
> color (#!2.2 & sel) #63ff75ff
> color (#!2.2 & sel) #64ff5cff
> color (#!2.2 & sel) #50ff3dff
> color (#!2.2 & sel) #50ff3cff
> color (#!2.2 & sel) #52ff37ff
> color (#!2.2 & sel) #50ff35ff
> color (#!2.2 & sel) #55ff2fff
> color (#!2.2 & sel) #5aff2cff
> color (#!2.2 & sel) #57ff29ff
> color (#!2.2 & sel) #59ff26ff
> color (#!2.2 & sel) #58fd26ff
> color (#!2.2 & sel) #57fa25ff
> color (#!2.2 & sel) #56f825ff
> color (#!2.2 & sel) #53f024ff
> color (#!2.2 & sel) #52eb23ff
> color (#!2.2 & sel) #50e522ff
> color (#!2.2 & sel) #4ee122ff
> color (#!2.2 & sel) #4ddd21ff
> color (#!2.2 & sel) #4bd820ff
> color (#!2.2 & sel) #49d31fff
> color (#!2.2 & sel) #48ce1fff
> color (#!2.2 & sel) #47cb1eff
> color (#!2.2 & sel) #46c81eff
> color (#!2.2 & sel) #45c61eff
> color (#!2.2 & sel) #44c31dff
> color (#!2.2 & sel) #43c11dff
> color (#!2.2 & sel) #42bf1cff
> color (#!2.2 & sel) #42be1cff
> color (#!2.2 & sel) #41ba1cff
> color (#!2.2 & sel) #40b91cff
> color (#!2.2 & sel) #40b81bff
> color (#!2.2 & sel) #3fb61bff
> color (#!2.2 & sel) #3fb51bff
> color (#!2.2 & sel) #3eb31bff
> color (#!2.2 & sel) #3db01aff
> color (#!2.2 & sel) #3daf1aff
> color (#!2.2 & sel) #3cad1aff
> color (#!2.2 & sel) #3cac1aff
> color (#!2.2 & sel) #3bab19ff
> color (#!2.2 & sel) #3aa619ff
> color (#!2.2 & sel) #38a218ff
> color (#!2.2 & sel) #379e18ff
> color (#!2.2 & sel) #359917ff
> color (#!2.2 & sel) #349616ff
> color (#!2.2 & sel) #359817ff
> color (#!2.2 & sel) #369c17ff
> color (#!2.2 & sel) #3aa619ff
> color (#!2.2 & sel) #3aa819ff
> color (#!2.2 & sel) #3baa19ff
> color (#!2.2 & sel) #3aa819ff
> color (#!2.2 & sel) #3aa719ff
> color (#!2.2 & sel) #38a218ff
> color (#!2.2 & sel) #379e18ff
> color (#!2.2 & sel) #369c17ff
> color (#!2.2 & sel) #359817ff
> color (#!2.2 & sel) #349616ff
> color (#!2.2 & sel) #359817ff
> color (#!2.2 & sel) #359917ff
> color (#!2.2 & sel) #379d17ff
> color (#!2.2 & sel) #359d18ff
> color (#!2.2 & sel) #309d18ff
> color (#!2.2 & sel) #1d9d1aff
> color (#!2.2 & sel) #229d30ff
> color (#!2.2 & sel) #279d3bff
> color (#!2.2 & sel) #2b9d3eff
> color (#!2.2 & sel) #2e9d40ff
> color (#!2.2 & sel) #2e9d41ff
> color (#!2.2 & sel) #309d42ff
> color (#!2.2 & sel) #319d43ff
> color (#!2.2 & sel) #329d44ff
> color (#!2.2 & sel) #339d48ff
> color (#!2.2 & sel) #339d56ff
> color (#!2.2 & sel) #339d5dff
> color (#!2.2 & sel) #329d5fff
> color (#!2.2 & sel) #2f9d5dff
> color (#!2.2 & sel) #269d44ff
> color (#!2.2 & sel) #249d3cff
> color (#!2.2 & sel) #239d37ff
> color (#!2.2 & sel) #24a239ff
> color (#!2.2 & sel) #25a53aff
> color (#!2.2 & sel) #28b13eff
> color (#!2.2 & sel) #2bc244ff
> color (#!2.2 & sel) #2dcb48ff
> color (#!2.2 & sel) #31d94dff
> color (#!2.2 & sel) #33e551ff
> color (#!2.2 & sel) #34e752ff
> color (#!2.2 & sel) #34e852ff
> color (#!2.2 & sel) #34ea53ff
> color (#!2.2 & sel) #cce4f7ff
> color (#!2.2 & sel) #f9f9f9ff
> color (#!2.2 & sel) #f0f0f0ff
> color (#!2.2 & sel) #acc8c2ff
> color (#!2.2 & sel) #aec8a7ff
> color (#!2.2 & sel) #878898ff
> color (#!2.2 & sel) #d7c3e4ff
> color (#!2.2 & sel) #afeeeeff
> color (#!2.2 & sel) #98f5cbff
> color (#!2.2 & sel) #579973ff
> color (#!2.2 & sel) #98f5caff
> color (#!2.2 & sel) #9af9cdff
> color (#!2.2 & sel) #9af8ccff
> color (#!2.2 & sel) #8ee5bcff
> color (#!2.2 & sel) #8de3bbff
> color (#!2.2 & sel) #86d8b2ff
> color (#!2.2 & sel) #81d0abff
> color (#!2.2 & sel) #7bc6a3ff
> color (#!2.2 & sel) #76bf9dff
> color (#!2.2 & sel) #76be9cff
> color (#!2.2 & sel) #75bd9bff
> color (#!2.2 & sel) #74bc9bff
> color (#!2.2 & sel) #73ba99ff
> color (#!2.2 & sel) #72b897ff
> color (#!2.2 & sel) #70b494ff
> color (#!2.2 & sel) #6db091ff
> color (#!2.2 & sel) #6caf90ff
> color (#!2.2 & sel) #64a285ff
> color (#!2.2 & sel) #66a588ff
> color (#!2.2 & sel) #69aa8cff
> color (#!2.2 & sel) #70b595ff
> color (#!2.2 & sel) #73ba99ff
> color (#!2.2 & sel) #78c19fff
> color (#!2.2 & sel) #79c3a0ff
> color (#!2.2 & sel) #78c397ff
> color (#!2.2 & sel) #75c38bff
> color (#!2.2 & sel) #72c382ff
> color (#!2.2 & sel) #70c377ff
> color (#!2.2 & sel) #6ec371ff
> color (#!2.2 & sel) #72c36dff
> color (#!2.2 & sel) #78c36bff
> color (#!2.2 & sel) #7ec36aff
> color (#!2.2 & sel) #84c36aff
> color (#!2.2 & sel) #88c369ff
> color (#!2.2 & sel) #8bc369ff
> color (#!2.2 & sel) #88c369ff
> color (#!2.2 & sel) #81c36aff
> color (#!2.2 & sel) #78c36aff
> color (#!2.2 & sel) #73c36aff
> color (#!2.2 & sel) #70c36aff
> color (#!2.2 & sel) #6ac36dff
> color (#!2.2 & sel) #6ac370ff
> color (#!2.2 & sel) #6ac379ff
> color (#!2.2 & sel) #6bc381ff
> color (#!2.2 & sel) #6bc384ff
> color (#!2.2 & sel) #6bc381ff
> color (#!2.2 & sel) #6ac379ff
> color (#!2.2 & sel) #6ec36aff
> color (#!2.2 & sel) #7ac36aff
> color (#!2.2 & sel) #81c36aff
> color (#!2.2 & sel) #88c369ff
> color (#!2.2 & sel) #91c367ff
> color (#!2.2 & sel) #98c366ff
> color (#!2.2 & sel) #97c366ff
> color (#!2.2 & sel) #95c364ff
> color (#!2.2 & sel) #7fc360ff
> color (#!2.2 & sel) #6cc359ff
> color (#!2.2 & sel) #6cc358ff
> color (#!2.2 & sel) #6bc357ff
> color (#!2.2 & sel) #6ac356ff
> color (#!2.2 & sel) #67c353ff
> color (#!2.2 & sel) #67c33fff
> color (#!2.2 & sel) #67c33cff
> color (#!2.2 & sel) #65c33aff
> color (#!2.2 & sel) #61c33dff
> color (#!2.2 & sel) #4fc349ff
> color (#!2.2 & sel) #59c35dff
> color (#!2.2 & sel) #63c367ff
> color (#!2.2 & sel) #6dc370ff
> color (#!2.2 & sel) #71c374ff
> color (#!2.2 & sel) #77c379ff
> color (#!2.2 & sel) #7dc383ff
> color (#!2.2 & sel) #81c389ff
> color (#!2.2 & sel) #82c38aff
> color (#!2.2 & sel) #8cc392ff
> color (#!2.2 & sel) #8dc395ff
> color (#!2.2 & sel) #8fc397ff
> color (#!2.2 & sel) #91c398ff
> color (#!2.2 & sel) #91c399ff
> color (#!2.2 & sel) #8ac39dff
> color (#!2.2 & sel) #81c3a0ff
> color (#!2.2 & sel) #7ec3a3ff
> color (#!2.2 & sel) #7dc3a3ff
> color (#!2.2 & sel) #7cc3a2ff
> color (#!2.2 & sel) #7bc3a1ff
> color (#!2.2 & sel) #7ac3a1ff
> color (#!2.2 & sel) #79c3a0ff
> color (#!2.2 & sel) #77c39dff
> color (#!2.2 & sel) #6ac38eff
> color (#!2.2 & sel) #5cc37cff
> color (#!2.2 & sel) #59c37bff
> color (#!2.2 & sel) #59c37aff
> color (#!2.2 & sel) #58c37aff
> color (#!2.2 & sel) #57c379ff
> color (#!2.2 & sel) #50c37eff
> color (#!2.2 & sel) #4fc37dff
> color (#!2.2 & sel) #4ec37dff
> color (#!2.2 & sel) #4dc37cff
> color (#!2.2 & sel) #4cc37bff
> color (#!2.2 & sel) #4bc37bff
> color (#!2.2 & sel) #4ac37bff
> color (#!2.2 & sel) #45c380ff
> color (#!2.2 & sel) #43c37fff
> color (#!2.2 & sel) #43c37eff
> color (#!2.2 & sel) #41c37eff
> color (#!2.2 & sel) #3fc37cff
> color (#!2.2 & sel) #3ac37aff
> color (#!2.2 & sel) #33c376ff
> color (#!2.2 & sel) #31c375ff
> color (#!2.2 & sel) #2fc374ff
> color (#!2.2 & sel) #2fc379ff
> color (#!2.2 & sel) #2fc392ff
> color (#!2.2 & sel) #2fc3a3ff
> color (#!2.2 & sel) #2fc3aaff
> color (#!2.2 & sel) #31c3b7ff
> color (#!2.2 & sel) #32c3c3ff
> color (#!2.2 & sel) #32bcc3ff
> color (#!2.2 & sel) #32c1c3ff
> color (#!2.2 & sel) #32c3abff
> color (#!2.2 & sel) #32c397ff
> color (#!2.2 & sel) #32c37fff
> color (#!2.2 & sel) #32c367ff
> color (#!2.2 & sel) #32c34fff
> color (#!2.2 & sel) #32c33bff
> color (#!2.2 & sel) #39c332ff
> color (#!2.2 & sel) #40c332ff
> color (#!2.2 & sel) #4cc332ff
> color (#!2.2 & sel) #54c332ff
> color (#!2.2 & sel) #51c332ff
> color (#!2.2 & sel) #4cc332ff
> color (#!2.2 & sel) #47c332ff
> color (#!2.2 & sel) #3bc332ff
> color (#!2.2 & sel) #3bc231ff
> color (#!2.2 & sel) #3abd30ff
> color (#!2.2 & sel) #39ba2fff
> color (#!2.2 & sel) #37b52eff
> color (#!2.2 & sel) #36b12dff
> color (#!2.2 & sel) #36b02dff
> hide sel surfaces
[Repeated 1 time(s)]
> show sel surfaces
> select subtract #2.2
4 models selected
> select add #5.11
2209 atoms, 2215 bonds, 273 residues, 1 model selected
> show sel cartoons
> hide sel surfaces
> select clear
> select #5.11/n:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
369 atoms, 371 bonds, 45 residues, 2 models selected
> color (#!5.11 & sel) cyan
> show sel surfaces
> hide sel surfaces
> select add #5.11
2209 atoms, 2215 bonds, 273 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!2.1-6#!3.1-7#!5.8-13#!6.1-6 cartoons
> hide #!2 models
> show #!2 models
> hide #!5 models
> select add #6
10276 atoms, 10570 bonds, 1297 residues, 7 models selected
> show sel cartoons
> hide sel surfaces
> hide #!2 models
> select clear
[Repeated 1 time(s)]
> select add #6
10276 atoms, 10570 bonds, 1297 residues, 7 models selected
> view matrix models
> #6,0.58593,0.51537,0.62536,18.855,-0.76234,0.088861,0.64104,-28.661,0.2748,-0.85235,0.44496,-98.421
> view matrix models
> #6,0.55904,0.48085,0.67547,17.477,-0.80848,0.1354,0.57274,-26.674,0.18394,-0.86629,0.46445,-98.854
> view matrix models
> #6,0.52605,0.56164,0.63862,21.061,-0.81318,0.11232,0.57106,-27.702,0.249,-0.81973,0.5158,-96.766
> view matrix models
> #6,0.61308,0.47139,0.63397,16.909,-0.75396,0.10942,0.64775,-27.759,0.23597,-0.87511,0.42249,-99.442
> view matrix models
> #6,0.55184,0.5125,0.65789,18.878,-0.80905,0.13769,0.57138,-26.58,0.20225,-0.84757,0.49063,-98.023
> view matrix models
> #6,0.59439,0.49558,0.63332,18.018,-0.7692,0.12063,0.62752,-27.288,0.23459,-0.86014,0.4529,-98.716
> view matrix models
> #6,0.50628,0.56702,0.64975,21.401,-0.83839,0.14718,0.52483,-26.22,0.20196,-0.81045,0.54989,-96.219
> view matrix models
> #6,0.52448,0.59191,0.61201,22.363,-0.80719,0.11701,0.57858,-27.5,0.27085,-0.79747,0.53916,-95.819
> view matrix models
> #6,0.54882,0.52822,0.6479,19.551,-0.80888,0.13997,0.57107,-26.487,0.21097,-0.83749,0.50409,-97.585
> view matrix models
> #6,0.55923,0.58316,0.58923,21.834,-0.77133,0.10553,0.62762,-27.978,0.30382,-0.80547,0.50883,-96.352
> view matrix models
> #6,0.54325,0.58425,0.60294,21.934,-0.79107,0.11563,0.6007,-27.554,0.28124,-0.8033,0.52499,-96.188
> view matrix models
> #6,0.41991,0.63819,0.64528,24.76,-0.83021,-0.017123,0.55719,-33.537,0.36664,-0.76969,0.52264,-94.886
> view matrix models
> #6,0.4686,0.64821,0.60019,24.891,-0.77331,-0.027469,0.63343,-33.831,0.42709,-0.76096,0.4884,-94.803
> view matrix models
> #6,0.42868,0.67925,0.59569,26.344,-0.7957,-0.028418,0.60502,-33.926,0.42789,-0.73335,0.5283,-93.432
> view matrix models
> #6,0.4616,0.68842,0.55946,26.541,-0.75169,-0.031344,0.65878,-33.959,0.47105,-0.72463,0.50301,-93.238
> view matrix models
> #6,0.444,0.68716,0.57505,26.578,-0.77423,-0.028844,0.63225,-33.89,0.45104,-0.72593,0.51921,-93.195
> view matrix models
> #6,0.44666,0.69175,0.56744,26.747,-0.80063,0.025941,0.59859,-31.517,0.39936,-0.72167,0.56542,-92.713
> view matrix models
> #6,0.45088,0.68394,0.57353,26.412,-0.79038,0.0073681,0.61257,-32.315,0.41473,-0.7295,0.54389,-93.179
> view matrix models
> #6,0.45174,0.68558,0.57089,26.473,-0.79988,0.02784,0.59951,-31.431,0.39512,-0.72747,0.56096,-92.979
> select clear
Drag select of 684 residues
> select clear
Drag select of 626 residues
> color (#!6.1-6 & sel) yellow
> color (#!6.1-6 & sel) #2eb02cff
> color (#!6.1-6 & sel) #3fb02bff
> color (#!6.1-6 & sel) #74b026ff
> color (#!6.1-6 & sel) #79b026ff
> color (#!6.1-6 & sel) #87b026ff
> color (#!6.1-6 & sel) #84b026ff
> color (#!6.1-6 & sel) #7bb026ff
> color (#!6.1-6 & sel) #74b027ff
> color (#!6.1-6 & sel) #96b025ff
> color (#!6.1-6 & sel) #a2b025ff
> color (#!6.1-6 & sel) #a4b025ff
> color (#!6.1-6 & sel) #a9b024ff
> color (#!6.1-6 & sel) #aeb023ff
> color (#!6.1-6 & sel) #b0b022ff
> color (#!6.1-6 & sel) #b0a722ff
> color (#!6.1-6 & sel) #b0a422ff
> select clear
Drag select of 1297 residues
> show sel surfaces
> show #!5 models
> show #!2 models
> select clear
> graphics silhouettes false
> select add #5.11
2209 atoms, 2215 bonds, 273 residues, 1 model selected
> transparency (#!5.11 & sel) 40
> select #5.11/n:61@O
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
369 atoms, 371 bonds, 45 residues, 2 models selected
> transparency (#!5.11 & sel) 0
> select clear
> hide #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> show #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> show #!2.1-6#!3.1-7#!5.8-13#!6.1-6 cartoons
> hide #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
Drag select of 64 residues
> select up
1840 atoms, 1844 bonds, 228 residues, 5 models selected
> select up
2209 atoms, 2215 bonds, 273 residues, 5 models selected
> select down
1840 atoms, 1844 bonds, 228 residues, 6 models selected
> color (#!5.12 & sel) #d5e8f7ff
> color (#!5.12 & sel) #b8a9c8ff
> color (#!5.12 & sel) #b7a9c8ff
> color (#!5.12 & sel) #c3bac8ff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #bfb125ff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #09e0e0ff
> color (#!5.12 & sel) #71ff8fff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #7cff9bff
> color (#!5.12 & sel) #84ffa6ff
> color (#!5.12 & sel) #6cff88ff
> color (#!5.12 & sel) #d1e6f7ff
> color (#!5.12 & sel) #f0f0f0ff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #4b9858ff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #4d995bff
> color (#!5.12 & sel) #cfe5f7ff
> color (#!5.12 & sel) #506dffff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #506dffff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #00ff00ff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #00ff00ff
> color (#!5.12 & sel) #2ad839ff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #acaec2ff
> color (#!5.12 & sel) #afeeeeff
> color (#!5.12 & sel) #5be773ff
> color (#!5.12 & sel) #50ca65ff
> color (#!5.12 & sel) #67ff82ff
> select clear
Drag select of 34 residues
> select up
1588 atoms, 1591 bonds, 202 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> color (#!2.1 & sel) #ddecf8ff
> color (#!2.1 & sel) #f0f0f0ff
> color (#!2.1 & sel) #ffffffff
> color (#!2.1 & sel) #f0f0f0ff
> color (#!2.1 & sel) #ffffffff
> color (#!2.1 & sel) #f0f0f0ff
> color (#!2.1 & sel) #ffffffff
> color (#!2.1 & sel) #d3e7f7ff
> color (#!2.1 & sel) #f9f9f9ff
> color (#!2.1 & sel) #afeeeeff
> color (#!2.1 & sel) #49ac4eff
> color (#!2.1 & sel) #afeeeeff
> color (#!2.1 & sel) #396647ff
> color (#!2.1 & sel) #479e4fff
> color (#!2.1 & sel) #44944dff
> color (#!2.1 & sel) #469c4fff
> color (#!2.1 & sel) #afeeeeff
> color (#!2.1 & sel) #49a651ff
> color (#!2.1 & sel) #49a550ff
> select clear
Drag select of 78 residues
> select up
1840 atoms, 1844 bonds, 228 residues, 5 models selected
> select up
3859 atoms, 3868 bonds, 485 residues, 5 models selected
> select down
1840 atoms, 1844 bonds, 228 residues, 10 models selected
> color (#!5.13 & sel) #67ff82ff
Drag select of 76 residues
> select up
3214 atoms, 3220 bonds, 410 residues, 10 models selected
> select up
3300 atoms, 3306 bonds, 424 residues, 10 models selected
> color (#!2.6#!5.13 & sel) #49a550ff
Drag select of 105 residues
> select up
1840 atoms, 1844 bonds, 228 residues, 5 models selected
> color (#!5.8 & sel) #67ff82ff
Drag select of 25 residues
> select up
1583 atoms, 1586 bonds, 201 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> color (#!2.5 & sel) #49a550ff
Drag select of 32 residues
> select clear
Drag select of 53 residues
> select up
1840 atoms, 1844 bonds, 228 residues, 5 models selected
> color (#!5.9 & sel) #67ff82ff
Drag select of 40 residues
> select up
1607 atoms, 1610 bonds, 205 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> color (#!2.4 & sel) #49a550ff
Drag select of 87 residues
> select up
1840 atoms, 1844 bonds, 228 residues, 5 models selected
> color (#!5.10 & sel) #67ff82ff
Drag select of 43 residues
> select up
1588 atoms, 1591 bonds, 202 residues, 5 models selected
> select up
1650 atoms, 1653 bonds, 212 residues, 5 models selected
> color (#!2.3 & sel) #49a550ff
> show sel surfaces
> select clear
[Repeated 1 time(s)]
> hide #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> show #!2.1-6#!3.1-7#!5.8-13#!6.1-6 surfaces
> select clear
> hide #!2.1-6#!3.1-7#!5.8-13#!6.1-6 cartoons
> select #5.10/n:46@CD
1 atom, 1 residue, 1 model selected
> select #5.10/K:26@CD2
1 atom, 1 residue, 1 model selected
> select add #5
14904 atoms, 14943 bonds, 1850 residues, 8 models selected
> select subtract #5.11
12695 atoms, 12728 bonds, 1577 residues, 40 models selected
> transparency (#!5.8-10,12-13 & sel) 40
> select clear
> select #5.11/K:34@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
576 atoms, 576 bonds, 71 residues, 2 models selected
> transparency (#!5.11 & sel) 0
> select clear
> select #5.11/J:217@CB
1 atom, 1 residue, 1 model selected
> select #5.11/L:156@CD1
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
505 atoms, 505 bonds, 64 residues, 2 models selected
> select up
2209 atoms, 2215 bonds, 273 residues, 2 models selected
> transparency (#!5.11 & sel) 40
> select clear
> select #5.11/n:49@O
1 atom, 1 residue, 1 model selected
> select add #5.10/n:50@CA
2 atoms, 2 residues, 3 models selected
> select add #5.9/n:53@CB
3 atoms, 3 residues, 5 models selected
> select add #5.8/n:46@CB
4 atoms, 4 residues, 7 models selected
> select add #5.13/n:47@N
5 atoms, 5 residues, 9 models selected
> select add #5.12/n:54@N
6 atoms, 6 residues, 11 models selected
> select up
46 atoms, 40 bonds, 6 residues, 12 models selected
> select up
2214 atoms, 2226 bonds, 270 residues, 12 models selected
> transparency (#!5.8-13 & sel) 0
> select clear
> save "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_with_peripherals_green_movie.cxs"
——— End of log from Thu Jun 29 10:01:54 2023 ———
opened ChimeraX session
> turn z 45
> turn y 45
> ~turn y 45
Unknown command: ~turn y 45
> ui tool show "Side View"
> turn x 45
> turn x -45
[Repeated 1 time(s)]
> turn x 60
> turn z 60
> turn y 3 60
> turn z 3 60
> turn x 3 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -45
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -45
[Repeated 3 time(s)]
> turn z 3 180
> turn y 3 180
> turn x -45
[Repeated 1 time(s)]
> turn y 3 180
> turn y 3 90
> turn x -45
[Repeated 1 time(s)]
> turn y 3 120
> turn x 3 45
> turn x 3 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn y 3 90 center #6
> turn z 3 90 center #6
> turn y 3 90 coordinateSystem #6
> turn x 3 90 coordinateSystem #6
> turn z 3 90 coordinateSystem #6
> rocko turn z 15 60 rock 60 coordinatesystem #6
Unknown command: rocko turn z 15 60 rock 60 coordinatesystem #6
> rock 60 coordinatesystem #6
Expected an axis vector or a keyword
> alias rocko turn z 15 60 rock 60 coordinatesystem #6
> turn z 15 60 rock 60 coordinatesystem #6
Expected fewer arguments
> turn z 15 60 rock 60 coordinateSystem #6
> turn z 15 60 rock 60
[Repeated 3 time(s)]
> turn z 15 60 rock 60 coordinateSystem #5
> turn z 15 60 rock 60 coordinateSystem #6
> turn z 15 60 rock 60 coordinateSystem #1
> turn z 15 60 rock 60 coordinateSystem #3
> turn z 15 60 rock 60 coordinateSystem #5
> turn z 15 60 coordinateSystem #5
> turn z 2 45 coordinateSystem #5
> turn z 2 45 coordinateSystem #6
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -45
[Repeated 5 time(s)]
> turn x 45
[Repeated 1 time(s)]
> open C:\Users\grush/Desktop/Movie_ring_SNARES.cxc
> movie record supersample 3
> turn x -45
> wait 40
> turn x -45
> wait 40
> turn y 1 120
> wait
> turn x 1 45
> wait
> movie encode C:\Users\grush/Desktop/movieTest.mp4 quality high
Movie saved to C:\Users\grush/Desktop/movieTest.mp4
executed Movie_ring_SNARES.cxc
> open C:\Users\grush/Desktop/Movie_ring_SNARES.cxc
> movie record supersample 3
> turn x -45
> wait 40
> turn x -45
> wait 40
> turn y 1 120
> wait
> turn x 1 45
> wait
> movie encode C:\Users\grush/Desktop/movieTest.mp4 quality high
Movie saved to C:\Users\grush/Desktop/movieTest.mp4
executed Movie_ring_SNARES.cxc
> open C:\Users\grush/Desktop/Movie_ring_SNARES.cxc
> movie record supersample 3
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -45 1
[Repeated 7 time(s)]
> turn x -45 3
[Repeated 6 time(s)]
> turn x -45
[Repeated 2 time(s)]
> reverse turn x 1 45
Unknown command: reverse turn x 1 45
> turn x 1 45
> turn x step 1 -45
Expected a number or a keyword
> turn x -45
[Repeated 2 time(s)]
> turn x 45
[Repeated 1 time(s)]
> turn x -45
[Repeated 1 time(s)]
> turn x 45
[Repeated 1 time(s)]
> turn x 1 45
> turn x -45
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -45
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 45
> open C:\Users\grush/Desktop/Movie_ring_SNARES.cxc
> movie record supersample 3
Already recording a movie
> stop
> open C:\Users\grush/Desktop/Movie_ring_SNARES.cxc
> movie record supersample 3
Already recording a movie
> save "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Fig1_with_peripherals_green_movie.cxs"
——— End of log from Thu Jun 29 11:41:30 2023 ———
opened ChimeraX session
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 1 45
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> save "C:/Users/grush/Documents/Seminars/Munc13
> project/Model_paper/Jim's_presentation/For_movie_ringSNARES.cxs"
——— End of log from Tue Oct 24 00:42:49 2023 ———
opened ChimeraX session
> turn x 1 45
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -45
> turn x 1 45
[Repeated 1 time(s)]
QWindowsWindow::setGeometry: Unable to set geometry 1058x695+642+307 (frame:
1090x783+626+235) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY4". Resulting geometry: 1042x646+650+348 (frame:
1074x734+634+276) margins: 16, 72, 16, 16 minimum size: 600x248 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524319, y=524375), mintrack=POINT(x=632, y=336)))
> turn x -1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x -1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 1 -45
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 1 45
> turn x -45
> turn x 1 45
> ~struts turn x 1 45
> struts delete turn x 1 45
Expected an atoms specifier or a keyword
> ~turn x 1 45
Unknown command: ~turn x 1 45
> undo turn x 1 45
Expected fewer arguments
OpenGL version: 3.3.0 NVIDIA 512.78
OpenGL renderer: NVIDIA GeForce GTX 1650 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: HP
Model: HP Spectre x360 Convertible 15t-eb000
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 16,868,048,896
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.0
Babel: 2.13.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.7.22
cftime: 1.6.3
charset-normalizer: 3.3.1
ChimeraX-AddCharge: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49
ChimeraX-AtomicLibrary: 11.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202310201838
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
comtypes: 1.1.14
contourpy: 1.1.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.0
filelock: 3.9.0
fonttools: 4.43.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.4.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.11.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.7
wcwidth: 0.2.8
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → General Controls |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → "turn" arguments |
comment:2 by , 2 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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Hi Kirill,
--Eric