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Opened 3 years ago
Closed 3 years ago
#8762 closed defect (not a bug)
MD Viewer: self.atomLocation[0]: list index out of range
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-69-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6rc202303310103 (2023-03-31 01:03:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6rc202303310103 (2023-03-31)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/usuario/Escritorio/imagen_ChimeraX/cell/structures/structures/View_1_Cell_previo_a_movie.cxs
Log from Fri Mar 31 12:22:44 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open C:/Users/Usuario/Desktop/Thesis/Final_figures.cxs
Log from Thu Mar 30 22:25:22 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/Usuario/Desktop/Paper
> Cell/curadas/structures/I1_with_opsPEC.pdb" "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/I2_with_opsPEC.pdb" "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/I3_with_opsPEC.pdb" "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/I4_with_opsPEC.pdb"
Summary of feedback from opening C:/Users/Usuario/Desktop/Paper
Cell/curadas/structures/I1_with_opsPEC.pdb
---
warning | Ignored bad PDB record found on line 26280
TER
Summary of feedback from opening C:/Users/Usuario/Desktop/Paper
Cell/curadas/structures/I2_with_opsPEC.pdb
---
warnings | Ignored bad PDB record found on line 26280
TER
Ignored bad PDB record found on line 28233
TER
Ignored bad PDB record found on line 28493
TER
Summary of feedback from opening C:/Users/Usuario/Desktop/Paper
Cell/curadas/structures/I3_with_opsPEC.pdb
---
warnings | Ignored bad PDB record found on line 26280
TER
Ignored bad PDB record found on line 28233
TER
Ignored bad PDB record found on line 28493
TER
Summary of feedback from opening C:/Users/Usuario/Desktop/Paper
Cell/curadas/structures/I4_with_opsPEC.pdb
---
warnings | Ignored bad PDB record found on line 26280
TER
Ignored bad PDB record found on line 26937
TER
Ignored bad PDB record found on line 28233
TER
Ignored bad PDB record found on line 28493
TER
Chain information for I1_with_opsPEC.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
Chain information for I2_with_opsPEC.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
Chain information for I3_with_opsPEC.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
Chain information for I4_with_opsPEC.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> cartoon
> hide target a
> set bgColor white
> select #1/A#2/A#3/A#4/A
3072 atoms, 3428 bonds, 152 residues, 4 models selected
> select clear
> select #1/A#2/A#3/A#4/A
3072 atoms, 3428 bonds, 152 residues, 4 models selected
> surface sel
> ui tool show "Color Actions"
> color sel moccasin
> select clear
> select #1/B#2/B#3/B#4/B
3136 atoms, 3532 bonds, 152 residues, 4 models selected
> cartoon sel
> surface sel
> ui tool show "Color Actions"
> color sel light goldenrod yellow
> select clear
> select #1/I#2/I#3/I#4/I
1036 atoms, 1148 bonds, 56 residues, 4 models selected
> color sel lime
> surface sel
> select clear
> select #1/C#2/C#3/C#4/C
7200 atoms, 7288 bonds, 928 residues, 4 models selected
> color sel dark gray
> surface sel
> color (#!1-4 & sel) dark gray
> transparency (#!1-4 & sel) 50
> cartoon hide (#!1-4 & sel)
> select clear
> select #1/D#2/D#3/D#4/D
7124 atoms, 7212 bonds, 920 residues, 4 models selected
> select #1/D#2/D#3/D#4/D
7124 atoms, 7212 bonds, 920 residues, 4 models selected
> color sel dark gray
> surface sel
> color (#!1-4 & sel) dark gray
> transparency (#!1-4 & sel) 50
> cartoon hide (#!1-4 & sel)
> select clear
> select #1/E#2/E#3/E#4/E
42340 atoms, 43016 bonds, 5368 residues, 4 models selected
> color sel light gray
> surface sel
> transparency (#!1-4 & sel) 50
> color (#!1-4 & sel) light gray
> cartoon hide (#!1-4 & sel)
> transparency (#!1-4 & sel) 50
> select clear
> select #1/F#2/F#3/F#4/F
42224 atoms, 42256 bonds, 450 pseudobonds, 9262 residues, 7 models selected
> ui tool show "Color Actions"
> color sel ghost white
> surface (#!1-4 & sel)
> ui tool show "Color Actions"
> color sel ghost white
> select clear
> select #1/H#2/H#3/H#4/H
5180 atoms, 5304 bonds, 648 residues, 4 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H
Alignment identifier is 1/H
> sequence chain #2/H
Alignment identifier is 2/H
> sequence chain #3/H
Alignment identifier is 3/H
> sequence chain #4/H
Alignment identifier is 4/H
> color sel yellow
> select clear
> select coil
44980 atoms, 44932 bonds, 5871 residues, 4 models selected
> select clear
> select #1/H:3326
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/H:3326-3331
60 atoms, 63 bonds, 6 residues, 1 model selected
> select #1/H#2/H#3/H#4/H
5180 atoms, 5304 bonds, 648 residues, 4 models selected
> lighting soft
> select #1/B#2/B#3/B#4/B
3136 atoms, 3532 bonds, 152 residues, 4 models selected
> ui tool show "Color Actions"
> color sel alice blue
> color sel antique white
> color sel lavender blush
> color sel misty rose
> select clear
> select #1/B#2/B#3/B#4/B
3136 atoms, 3532 bonds, 152 residues, 4 models selected
> ui tool show "Color Actions"
> color sel light goldenrod yellow
> color sel light cyan
> color sel alice blue
> color sel mint cream
> color sel lemon chiffon
> select #1/F
10556 atoms, 10717 bonds, 1360 residues, 1 model selected
> select #2/F
10556 atoms, 10513 bonds, 150 pseudobonds, 2634 residues, 2 models selected
> select clear
> select #1/G#2/G#3/G#4/G
2624 atoms, 2595 bonds, 33 pseudobonds, 478 residues, 6 models selected
> ui tool show "Color Actions"
> color sel ghost white
> surface (#!1-4 & sel)
> ui tool show "Color Actions"
> color sel ghost white
> select clear
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!1 models
> save "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/Final_figures.cxs"
> select #1/B#2/B#3/B#4/B
3136 atoms, 3532 bonds, 152 residues, 4 models selected
> select #1/H#2/H#3/H#4/H
5180 atoms, 5304 bonds, 648 residues, 4 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H #2/H #3/H #4/H
Alignment identifier is 1
> color byattribute r:number :3424-3485
1964 atoms, 248 residues, atom number range 3.42e+03 to 3.48e+03
> select clear
> hide #!4 models
> hide #!3 models
> hide #!2 models
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting flat
> lighting soft
> lighting simple
> ui tool show "Show Sequence Viewer"
> sequence chain #1/H
Alignment identifier is 1/H
> sequence chain #2/H
Alignment identifier is 2/H
> sequence chain #3/H
Alignment identifier is 3/H
> sequence chain #4/H
Alignment identifier is 4/H
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> ui tool show "Side View"
> select #1/H:3324
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/H:3325
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/H:3324
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/H:3325
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/H:3325
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/H:3324
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> color #1 cyan
> undo
> select #1/H:3324
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> color sel cyan
> select clear
> select #1/H:3332
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/H:3332-3336
39 atoms, 38 bonds, 5 residues, 1 model selected
> color sel cyan
> select clear
> select #1/H:3347
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/H:3347-3376
229 atoms, 232 bonds, 30 residues, 1 model selected
> color sel cyan
> select clear
> select #1/H:3383
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/H:3383-3388
49 atoms, 50 bonds, 6 residues, 1 model selected
> color sel cyan
> select clear
> select #1/H:3394
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/H:3394-3403
79 atoms, 80 bonds, 10 residues, 1 model selected
> color sel cyan
> select clear
> select #1/H:3413
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/H:3404-3413
66 atoms, 68 bonds, 10 residues, 1 model selected
> color sel cyan
> select #1/H:3422
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/H:3422-3444
178 atoms, 183 bonds, 23 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #1/H:3422-3444
178 atoms, 183 bonds, 23 residues, 1 model selected
> select clear
> show #!2 models
> select #2/H:3324
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> color sel cyan
> select #2/H:3332
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/H:3332-3336
39 atoms, 38 bonds, 5 residues, 1 model selected
> color sel cyan
> select #2/H:3347
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/H:3347-3349
21 atoms, 20 bonds, 3 residues, 1 model selected
> color sel cyan
> select clear
> select #2/H:3341
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/H:3341
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel cyan
> hide #!1 models
> select clear
> select #2/H:3347
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/H:3347-3349
21 atoms, 20 bonds, 3 residues, 1 model selected
> color sel cyan
> select clear
> select #2/H:3353
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/H:3353-3376
186 atoms, 189 bonds, 24 residues, 1 model selected
> color sel cyan
> select clear
> select #2/H:3383
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:3383-3388
49 atoms, 50 bonds, 6 residues, 1 model selected
> color sel cyan
> select clear
> select #2/H:3394
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/H:3394-3412
139 atoms, 143 bonds, 19 residues, 1 model selected
> color sel cyan
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> select #3/H:3344
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/H:3324-3344
185 atoms, 189 bonds, 21 residues, 1 model selected
> color sel cyan
> select clear
> select #3/H:3348
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/H:3348-3390
341 atoms, 349 bonds, 43 residues, 1 model selected
> color sel cyan
> select clear
> select #3/H:3394-3395
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/H:3394-3414
150 atoms, 154 bonds, 21 residues, 1 model selected
> color sel cyan
> select clear
> 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
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!4 models
> select #4/H:3325
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/H:3324-3325
17 atoms, 16 bonds, 2 residues, 1 model selected
> color sel cyan
> select #4/H:3333
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/H:3333-3336
33 atoms, 32 bonds, 4 residues, 1 model selected
> color sel cyan
> select clear
> select #4/H:3347
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/H:3347-3349
21 atoms, 20 bonds, 3 residues, 1 model selected
> color sel cyan
> select #4/H:3353
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/H:3353-3357
35 atoms, 35 bonds, 5 residues, 1 model selected
> color sel cyan
> select #4/H:3361
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/H:3361-3366
50 atoms, 49 bonds, 6 residues, 1 model selected
> color sel cyan
> select #4/H:3370-3371
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/H:3370-3376
56 atoms, 58 bonds, 7 residues, 1 model selected
> color sel cyan
> select #4/H:3383-3384
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/H:3383-3389
56 atoms, 57 bonds, 7 residues, 1 model selected
> color sel cyan
> hide #!3 models
> select #4/H:3394
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/H:3394-3397
27 atoms, 26 bonds, 4 residues, 1 model selected
> color sel cyan
> select #4/H:3402
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/H:3402-3413
84 atoms, 86 bonds, 12 residues, 1 model selected
> color sel cyan
> select #4/H:3420
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/H:3420-3421
13 atoms, 12 bonds, 2 residues, 1 model selected
> select clear
> save "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/Final_figures.cxs"
> show #!1 models
> hide #!4 models
> select #1/A:1
16 atoms, 17 bonds, 1 residue, 1 model selected
> select clear
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #1/H:3417-3421
40 atoms, 40 bonds, 5 residues, 1 model selected
> select #1/H:3414-3421
60 atoms, 60 bonds, 8 residues, 1 model selected
> select #1/H:3414-3420
53 atoms, 53 bonds, 7 residues, 1 model selected
> select #1/H:3414-3420
53 atoms, 53 bonds, 7 residues, 1 model selected
> show #!1 models
> hide #!4 models
> select clear
> select #1/H:3421
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #1/H:3421
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> select clear
> select #1/H:3420
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> select #1/B#2/B#3/B#4/B
3136 atoms, 3532 bonds, 152 residues, 4 models selected
> ui tool show "Color Actions"
> color sel moccasin
> select #1/A#2/A#3/A#4/A
3072 atoms, 3428 bonds, 152 residues, 4 models selected
> color sel lemon chiffon
> select clear
> select #1/B#2/B#3/B#4/B
3136 atoms, 3532 bonds, 152 residues, 4 models selected
> cartoon hide (#!1 & sel)
> select #1/A#2/A#3/A#4/A
3072 atoms, 3428 bonds, 152 residues, 4 models selected
> cartoon hide (#!1 & sel)
> select clear
> lighting simple
> lighting soft
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!4 models
> save "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/Final_figures.cxs"
[Repeated 1 time(s)]
> hide #!4 models
> hide #!3 models
> hide #!2 models
> open "C:/Users/Usuario/Desktop/Paper
> Cell/Chimera_sessions/opsPEC_RfaH_active_SMOG.pdb"
> "C:/Users/Usuario/Desktop/Paper
> Cell/Chimera_sessions/opsPEC_RfaH_recruited_SMOG.pdb"
Summary of feedback from opening C:/Users/Usuario/Desktop/Paper
Cell/Chimera_sessions/opsPEC_RfaH_active_SMOG.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK File generated with: smog_adjustPDB -i opsPEC_RfaH_active_asMG.pdb -o
opsPEC_RfaH_active_SMOG.pdb
Ignored bad PDB record found on line 2
REMARK Generated on Tue Jan 17 17:10:12 -03 2023. Hostname: 201-5-190-eduroam-
pf.wlan.net.uc.cl
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
17894 messages similar to the above omitted
Summary of feedback from opening C:/Users/Usuario/Desktop/Paper
Cell/Chimera_sessions/opsPEC_RfaH_recruited_SMOG.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK File generated with: smog_adjustPDB -i opsPEC_RfaH_recruited_asMG.pdb
-o opsPEC_RfaH_recruited_SMOG.pdb
Ignored bad PDB record found on line 2
REMARK Generated on Tue Jan 17 17:10:32 -03 2023. Hostname: 201-5-190-eduroam-
pf.wlan.net.uc.cl
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
17894 messages similar to the above omitted
Chain information for opsPEC_RfaH_active_SMOG.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
Chain information for opsPEC_RfaH_recruited_SMOG.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> select #5/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> cartoon sel
> hide sel target a
> select #5/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> cartoon sel
> hide sel target a
> select #6/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> cartoon sel
> hide sel target a
> select #6/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> cartoon sel
> hide sel target a
> hide #!1 models
> select clear
> select add #5
28484 atoms, 29107 bonds, 3499 residues, 1 model selected
> select add #6
56968 atoms, 58214 bonds, 6998 residues, 2 models selected
> surface sel
> hide (#!5-6 & sel) target a
> transparency (#!5-6 & sel) 50
> hide #!5 models
> hide #!6 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> show #!6 models
> select clear
> select #5/I
257 atoms, 287 bonds, 12 residues, 1 model selected
> transparency (#!5 & sel) 40
> color (#!5 & sel) lime
> select #5/I
257 atoms, 287 bonds, 12 residues, 1 model selected
> select #6/I
257 atoms, 287 bonds, 12 residues, 1 model selected
> transparency (#!6 & sel) 40
> surface (#!6 & sel)
> transparency (#!6 & sel) 40
> surface (#!6 & sel)
> show (#!6 & sel) target ab
> surface (#!6 & sel)
> hide (#!6 & sel) target a
> color (#!6 & sel) lime
> select #1/C#2/C#3/C#4/C#5/C#6/C
10800 atoms, 10932 bonds, 1392 residues, 6 models selected
> color (#!5-6 & sel) dark gray
> transparency (#!5-6 & sel) 50
> select #1/G#2/G#3/G#4/G#5/G#6/G
3936 atoms, 3911 bonds, 33 pseudobonds, 644 residues, 8 models selected
> color (#!5-6 & sel) gray
> transparency (#!5-6 & sel) 50
> select #1/D#2/D#3/D#4/D#5/D#6/D
10686 atoms, 10818 bonds, 1380 residues, 6 models selected
> color (#!5-6 & sel) dark gray
> transparency (#!5-6 & sel) 50
> select clear
> select #1/E#2/E#3/E#4/E#5/E#6/E
63510 atoms, 64524 bonds, 8052 residues, 6 models selected
> color (#!5-6 & sel) light gray
> transparency (#!5-6 & sel) 50
> color (#!5-6 & sel) light gray
> transparency (#!5-6 & sel) 50
> select clear
[Repeated 2 time(s)]
> show #!1 models
> hide #!1 models
> select #1/F#2/F#3/F#4/F#5/F#6/F
63336 atoms, 63690 bonds, 450 pseudobonds, 11982 residues, 9 models selected
> ui tool show "Color Actions"
> color sel ghost white
> select clear
> select #1/H#2/H#3/H#4/H#5/H#6/H
7770 atoms, 7956 bonds, 972 residues, 6 models selected
> select add #6
34959 atoms, 35737 bonds, 4309 residues, 8 models selected
> select subtract #6
6475 atoms, 6630 bonds, 810 residues, 15 models selected
> select add #6
34959 atoms, 35737 bonds, 4309 residues, 7 models selected
> select subtract #6
6475 atoms, 6630 bonds, 810 residues, 15 models selected
> select add #5
33664 atoms, 34411 bonds, 4147 residues, 6 models selected
> select subtract #5
5180 atoms, 5304 bonds, 648 residues, 13 models selected
> select add #4
32369 atoms, 32859 bonds, 170 pseudobonds, 5332 residues, 5 models selected
> select add #3
59558 atoms, 60421 bonds, 333 pseudobonds, 10016 residues, 14 models selected
> select add #2
86747 atoms, 87998 bonds, 483 pseudobonds, 14627 residues, 23 models selected
> select add #1
113936 atoms, 115779 bonds, 483 pseudobonds, 17964 residues, 31 models
selected
> select subtract #1
85452 atoms, 86672 bonds, 483 pseudobonds, 14465 residues, 38 models selected
> select subtract #2
56968 atoms, 57769 bonds, 333 pseudobonds, 9692 residues, 28 models selected
> select subtract #3
28484 atoms, 28881 bonds, 170 pseudobonds, 4846 residues, 18 models selected
> select subtract #4
8 models selected
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> cartoon (#!5 & sel)
> transparency (#!5 & sel) 90
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> select #6/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> transparency (#!6 & sel) 50
> transparency (#!6 & sel) 90
> cartoon (#!6 & sel)
> select clear
> select #5/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> surface (#!5 & sel)
> cartoon hide (#!5 & sel)
> select #6/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> cartoon hide (#!6 & sel)
> select #5/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> cartoon hide (#!5 & sel)
> select #6/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> cartoon hide (#!6 & sel)
> select clear
> show #!4 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> hide #!4 models
> select #5/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> ui tool show "Color Actions"
> color sel moccasin
> select #6/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> ui tool show "Color Actions"
> color sel moccasin
> select #5/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pink
> color sel peach puff
> color sel linen
> color sel lemon chiffon
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lemon chiffon
> select clear
> hide #!6 models
> show #!5 models
> show #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/Final_figures.cxs"
> hide #!1 models
> show #!5 models
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> surface hidePatches (#!5 & sel)
> color (#!5 & sel) yellow
> hide #!5 models
> show #!6 models
> select #6/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> surface hidePatches (#!6 & sel)
> color (#!6 & sel) yellow
> select clear
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> show #!5 models
> hide #!6 models
> color byattribute r:number :3424-3485
1964 atoms, 248 residues, atom number range 3.42e+03 to 3.48e+03
> color byattribute r:number :101-162
6776 atoms, 868 residues, 14 surfaces, atom number range 101 to 162
> select clear
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/H
Alignment identifier is 5/H
> select #5/H:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:101-162
491 atoms, 501 bonds, 62 residues, 1 model selected
> select #5/H:101
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:101-162
491 atoms, 501 bonds, 62 residues, 1 model selected
> color byattribute r:number
170904 atoms, 24962 residues, 50 surfaces, atom number range 1 to 3.5e+03
> select clear
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> select add #5
28484 atoms, 29107 bonds, 3499 residues, 1 model selected
> select subtract #5
9 models selected
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> select color byattribute r:number :101-162
Expected an objects specifier or a keyword
> select r:number :101-162
Expected an objects specifier or a keyword
> select clear
> save "C:/Users/Usuario/Desktop/Paper
> Cell/curadas/structures/Final_figures.cxs"
——— End of log from Thu Mar 30 22:25:22 2023 ———
opened ChimeraX session
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> select add #6
29779 atoms, 30433 bonds, 3661 residues, 3 models selected
> select subtract #6
1295 atoms, 1326 bonds, 162 residues, 11 models selected
Alignment identifier is 5/H
> select #6/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
Alignment identifier is 6/H
> select clear
> select #5/H:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/H:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:10-13
33 atoms, 32 bonds, 4 residues, 1 model selected
> select #5/H:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> color (#!5 & sel) cyan
> select #5/H:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/H:11-13
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #5/H:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:24-26
21 atoms, 20 bonds, 3 residues, 1 model selected
> color (#!5 & sel) cyan
> select #5/H:13
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:10-13
33 atoms, 32 bonds, 4 residues, 1 model selected
> color (#!5 & sel) cyan
> select clear
> select #5/H:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:37-38
17 atoms, 16 bonds, 2 residues, 1 model selected
> color (#!5 & sel) cyan
> select #5/H:43
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/H:43-44
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #5/H:42
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:42-44
27 atoms, 26 bonds, 3 residues, 1 model selected
> color (#!5 & sel) cyan
> select #5/H:51
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/H:51-53
26 atoms, 27 bonds, 3 residues, 1 model selected
> select #5/H:52-53
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/H:50-53
34 atoms, 35 bonds, 4 residues, 1 model selected
> color (#!5 & sel) cyan
> select clear
> select #5/H:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:60-74
113 atoms, 114 bonds, 15 residues, 1 model selected
> color (#!5 & sel) cyan
> select #5/H:79
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:79-89
78 atoms, 80 bonds, 11 residues, 1 model selected
> color (#!5 & sel) cyan
> select clear
> select #5/H:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:98-105
67 atoms, 68 bonds, 8 residues, 1 model selected
> color (#!5 & sel) cyan
> select #5/H:110
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:110-113
30 atoms, 32 bonds, 4 residues, 1 model selected
> select #5/H:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:112-113
11 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/H:112-113
11 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/H:110
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:110
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:110
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:109-110
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/H:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:113
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/H:109-113
37 atoms, 39 bonds, 5 residues, 1 model selected
> color (#!5 & sel) cyan
> select clear
> select #5/H:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> color byattribute r:number :101-162
6776 atoms, 868 residues, 14 surfaces, atom number range 101 to 162
> select clear
> select #5/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> color byattribute r:number :101-162
6776 atoms, 868 residues, 14 surfaces, atom number range 101 to 162
> select color byattribute r:number :101-162
Expected an objects specifier or a keyword
> color #5 byattribute r:number :101-162
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color byattribute #5 r:number :101-162
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> select clear
[Repeated 1 time(s)]
> select #5
28484 atoms, 29107 bonds, 3499 residues, 1 model selected
> select #5H
Expected an objects specifier or a keyword
> select #5.H
Expected an objects specifier or a keyword
> select #5,H
Expected an objects specifier or a keyword
> select #5@H
Nothing selected
> select #5
28484 atoms, 29107 bonds, 3499 residues, 1 model selected
> select clear
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/H:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/H:1-2
17 atoms, 16 bonds, 2 residues, 1 model selected
> color (#!6 & sel) cyan
> select #6/H:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/H:10-11
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #6/H:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/H:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/H:12-13
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/H:12-13
13 atoms, 12 bonds, 2 residues, 1 model selected
> color (#!6 & sel) cyan
> select #6/H:25
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/H:25-26
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #6/H:25
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/H:24-25
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/H:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/H:24-26
21 atoms, 20 bonds, 3 residues, 1 model selected
> color (#!6 & sel) cyan
> select #6/H:30
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/H:30-53
186 atoms, 189 bonds, 24 residues, 1 model selected
> color (#!6 & sel) cyan
> select clear
> select #6/H:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/H:60-65
49 atoms, 50 bonds, 6 residues, 1 model selected
> color (#!6 & sel) cyan
> select #6/H:71
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/H:71-74
27 atoms, 26 bonds, 4 residues, 1 model selected
> color (#!6 & sel) cyan
> select #6/H:89
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/H:79-89
78 atoms, 80 bonds, 11 residues, 1 model selected
> color (#!6 & sel) cyan
> select clear
> select #6/H:115
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/H:115
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/H:113-114
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #6/H:111-114
31 atoms, 32 bonds, 4 residues, 1 model selected
> select #6/H:108-111
32 atoms, 33 bonds, 4 residues, 1 model selected
> select #6/H:108-111
32 atoms, 33 bonds, 4 residues, 1 model selected
> select #6/H:107
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/H:100-107
63 atoms, 64 bonds, 8 residues, 1 model selected
> select #6/H:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/H:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/H:125-162
309 atoms, 313 bonds, 38 residues, 1 model selected
> select #6/H:125-154
236 atoms, 239 bonds, 30 residues, 1 model selected
> select #6/H:125-155
245 atoms, 248 bonds, 31 residues, 1 model selected
> select #6/H:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/H:161-162
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #6/H:159
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/H:154-159
51 atoms, 51 bonds, 6 residues, 1 model selected
> color (#!6 & sel) cyan
> select clear
> select #6/H:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/H:160-162
29 atoms, 28 bonds, 3 residues, 1 model selected
> color (#!6 & sel) cyan
> select clear
> select #6/H:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:11@C4'
1 atom, 1 residue, 1 model selected
> select #6/H:11
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #6/H:10
20 atoms, 18 bonds, 2 residues, 2 models selected
> color (#!6 & sel) cyan
> select clear
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5
28484 atoms, 29107 bonds, 3499 residues, 1 model selected
> select #5:101-162
2442 atoms, 2482 bonds, 310 residues, 1 model selected
> color byattribute r:number
170904 atoms, 24962 residues, 50 surfaces, atom number range 1 to 3.5e+03
> select #5.H:101-162
Expected an objects specifier or a keyword
> select #5:101-162.H
Expected an objects specifier or a keyword
> select #5:101-162.h
Expected an objects specifier or a keyword
> select clear
> color byattribute r:number :101-162.h
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute r:number H:101-162
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute r:number H:101-162
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute r:number :101-162
6776 atoms, 868 residues, 14 surfaces, atom number range 101 to 162
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> select #1/E#2/E#3/E#4/E#5/E#6/E
63510 atoms, 64524 bonds, 8052 residues, 6 models selected
> color (#!5-6 & sel) light gray
> transparency (#!5-6 & sel) 50
> select clear
> select #1/F#2/F#3/F#4/F#5/F#6/F
63336 atoms, 63690 bonds, 450 pseudobonds, 11982 residues, 9 models selected
> color (#!5-6 & sel) white
> ui tool show "Color Actions"
> color sel ghost white
> select clear
> select #1/C#2/C#3/C#4/C#5/C#6/C
10800 atoms, 10932 bonds, 1392 residues, 6 models selected
> color (#!5-6 & sel) dark gray
> transparency (#!5-6 & sel) 50
> select clear
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/A:16@C2'
1 atom, 1 residue, 1 model selected
> select #6/A:16@C7
1 atom, 1 residue, 1 model selected
> select add #6/A:16@C2'
2 atoms, 1 residue, 2 models selected
> select add #6/A:16@O4
3 atoms, 1 residue, 2 models selected
> transparency (#!6 & sel) 30
> select clear
> undo
[Repeated 1 time(s)]
> transparency (#!6 & sel) 0
> select clear
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> save C:/Users/Usuario/Desktop/Thesis/alpha_Intermediarios_beta.cxs
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> select #6/H:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!6 & sel) magenta
> select clear
> select #6/H:97
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> select clear
> ui tool show "Side View"
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #5/H:98
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!5 & sel) magenta
> select #5/H:97
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> select clear
> show #!6 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #4/H:3421
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> select #4/H:3420
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> select clear
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> select #3/H:3420
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> select #3/H:3421
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel magenta
> select clear
[Repeated 1 time(s)]
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!6 models
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!1 models
> show #!3 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #!3 models
> hide #!5 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 1/F
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11
Alignment identifier is 12
Alignment identifier is 13
Alignment identifier is 14
Alignment identifier is 15
Alignment identifier is 16
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!2 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!3 models
> lighting simple
> lighting soft
> lighting full
> show #!6 models
> hide #!5 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!6 models
> hide #!5 models
> select #4/H:3417
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/H:3416
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> show (#!3 & sel) target ab
> surface hidePatches (#!3 & sel)
[Repeated 1 time(s)]
> cartoon (#!3 & sel)
> select #3/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> surface hidePatches (#!3 & sel)
> select #4/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> surface hidePatches (#!4 & sel)
> hide (#!4 & sel) target a
> select #4/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> surface hidePatches (#!4 & sel)
> select #3/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> hide (#!3 & sel) target a
> nucleotides (#!3 & sel) fill
> show (#!3 & sel) target ab
> style (#!3 & sel) ringFill thick
Changed 38 residue ring styles
> style (#!3 & sel) stick
Changed 768 atom styles
> nucleotides (#!3 & sel) fill
> color (#!3 & sel) byelement
> select #4/F:2027@CG
1 atom, 1 residue, 1 model selected
> hide #!3 models
> show #!3 models
> hide #!4 models
> select #3/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> style (#!3 & sel) stick
Changed 784 atom styles
> show (#!3 & sel) target ab
> nucleotides (#!3 & sel) fill
> color (#!3 & sel) byelement
> color (#!3 & sel) byhetero
> select #3@@serial_number=16905
1 atom, 1 residue, 1 model selected
> select #3@@serial_number=16905
1 atom, 1 residue, 1 model selected
> select clear
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> lighting simple
> hide #!5 models
> hide #!4 models
> save C:/Users/Usuario/Desktop/Thesis/I3_inside.png width 2235 height 2235
> supersample 3 transparentBackground true
> show #!4 models
> hide #!3 models
> save C:/Users/Usuario/Desktop/Thesis/I4_inside.png width 2235 height 2235
> supersample 3 transparentBackground true
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> save C:/Users/Usuario/Desktop/Thesis/Active_beta_inside.png width 2235
> height 2235 supersample 3
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!2 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #6/H:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #6/H:28
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add #6/H:29
22 atoms, 19 bonds, 3 residues, 2 models selected
> select add #2/H:3350
30 atoms, 26 bonds, 4 residues, 3 models selected
> select add #2/H:3351
36 atoms, 31 bonds, 5 residues, 3 models selected
> select add #2/H:3352
44 atoms, 38 bonds, 6 residues, 3 models selected
> hide #!1 models
> hide #!6 models
> hide #!2 models
> show #!1 models
> select #1/H:3352
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/H:3351
14 atoms, 12 bonds, 2 residues, 1 model selected
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> select #1/H:3350
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/H:3351
14 atoms, 12 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> show #!2 models
> select #2/H:3351
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/H:3352
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/H:3351
14 atoms, 12 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select #2/A:10@C4'
1 atom, 1 residue, 1 model selected
> show #!6 models
> select #6/H:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/H:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #6/H:28
14 atoms, 12 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select #2@@serial_number=18131
1 atom, 1 residue, 1 model selected
> select #2/E:913@CB
1 atom, 1 residue, 1 model selected
> select clear
> hide #!2 models
> hide #!1 models
> hide #!6 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> select #3/H:3419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/H:3418
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #3/H:3417
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add #3/H:3416
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add #3/H:3415
42 atoms, 38 bonds, 5 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> show #!4 models
> hide #!3 models
> select #4/H:3419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/H:3418
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4/H:3419
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #4/H:3417
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add #4/H:3416
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add #4/H:3415
42 atoms, 38 bonds, 5 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> hide #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!4 models
> show #!5 models
> select #5/H:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5/H:95
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #5/H:94
27 atoms, 25 bonds, 3 residues, 2 models selected
> select add #5/H:92
34 atoms, 31 bonds, 4 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!6 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!6 models
> ui tool show "Side View"
> lighting soft
> save C:/Users/Usuario/Desktop/Thesis/Recruited.png width 2235 height 2235
> supersample 3 transparentBackground true
> ui tool show "Side View"
[Repeated 1 time(s)]
> show #!1 models
> show #!2 models
> show #!3 models
> save C:/Users/Usuario/Desktop/Thesis/Figure_Cell.cxs
> show #!4 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> hide #!6 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #4/I
259 atoms, 287 bonds, 14 residues, 1 model selected
> cartoon (#!4 & sel)
> surface hidePatches (#!4 & sel)
> select clear
> show #!5 models
> hide #!4 models
> show #!3 models
> hide #!5 models
> save C:/Users/Usuario/Desktop/Thesis/Recruited.png width 2235 height 1156
> supersample 3 transparentBackground true
> show #!4 models
> hide #!3 models
> save C:/Users/Usuario/Desktop/Thesis/I4_inside.png width 2235 height 1156
> supersample 3 transparentBackground true
> hide #!4 models
> show #!5 models
> save C:/Users/Usuario/Desktop/Thesis/Active_beta.png width 2235 height 1156
> supersample 3 transparentBackground true
> show #!6 models
> hide #!5 models
> save C:/Users/Usuario/Desktop/Thesis/Recruited_alfa.png width 2235 height
> 1156 supersample 3 transparentBackground true
> show #!1 models
> hide #!6 models
> save C:/Users/Usuario/Desktop/Thesis/I1_inside.png width 2235 height 1156
> supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> save C:/Users/Usuario/Desktop/Thesis/I2_inside.png width 2235 height 1156
> supersample 3 transparentBackground true
> show #!1 models
> hide #!2 models
> save C:/Users/Usuario/Desktop/Thesis/I1_inside.png width 2235 height 1156
> supersample 3 transparentBackground true
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!5 models
> show #!6 models
> show #!4 models
> select #1/A#2/A#3/A#4/A#5/A#6/A
4608 atoms, 5142 bonds, 228 residues, 6 models selected
> surface (#!1-6 & sel)
> cartoon hide (#!1-6 & sel)
[Repeated 1 time(s)]
> hide (#!1-6 & sel) target a
> style (#!1-6 & sel) stick
Changed 4608 atom styles
> hide #!1 models
> cartoon hide (#!2-6 & sel)
> surface hidePatches (#!2-6 & sel)
> show #!1 models
> hide #!1 models
> select clear
> select #4/B:39
19 atoms, 21 bonds, 1 residue, 1 model selected
> show #!1 models
> select #4/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> cartoon hide (#!4 & sel)
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> select #4/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> select #4/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> cartoon #3
> surface #3
> undo
> transparency #3 100
> select clear
> save C:/Users/Usuario/Desktop/Thesis/other_way.png width 2235 height 1156
> supersample 3 transparentBackground true
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select #3/B
784 atoms, 883 bonds, 38 residues, 1 model selected
> hide (#!3 & sel) target a
> select #3/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> view sel
> cartoon (#!3 & sel)
> select clear
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> hide #!4 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> select #5/H:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:28
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5/H:29
14 atoms, 12 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> select #6/H:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/H:95
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/H:96
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #6/H:94
27 atoms, 25 bonds, 3 residues, 2 models selected
> select add #6/H:93
35 atoms, 32 bonds, 4 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/H:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> view clip false
> select clear
> show #!5 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #4/H:3352
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/H:3351
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #4/H:3352
14 atoms, 12 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> show #!3 models
> hide #!4 models
> hide #!5 models
> select #3/H:3352@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #3/A
768 atoms, 857 bonds, 38 residues, 1 model selected
> surface (#!3 & sel)
> transparency (#!3 & sel) 0
> hide (#!3 & sel) target a
> style (#!3 & sel) stick
Changed 768 atom styles
> ui tool show "Color Actions"
> color sel moccasin
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/A#2/A#3/A#4/A#5/A#6/A
4608 atoms, 5142 bonds, 228 residues, 6 models selected
> surface hidePatches (#!1,4 & sel)
> select #1/B#2/B#3/B#4/B#5/B#6/B
4704 atoms, 5298 bonds, 228 residues, 6 models selected
> surface hidePatches (#!1,4 & sel)
> show #!2 models
> show #!3 models
> show #!5 models
> show #!6 models
> select #1/A#2/A#3/A#4/A#5/A#6/A
4608 atoms, 5142 bonds, 228 residues, 6 models selected
> surface hidePatches (#!1-6 & sel)
> cartoon (#!1-6 & sel)
> select #1/B#2/B#3/B#4/B#5/B#6/B
4704 atoms, 5298 bonds, 228 residues, 6 models selected
> surface hidePatches (#!1-6 & sel)
> select clear
> select #1/B#2/B#3/B#4/B#5/B#6/B
4704 atoms, 5298 bonds, 228 residues, 6 models selected
> ui tool show "Color Actions"
> color sel moccasin
> surface (#!1-6 & sel)
> select clear
> select #1/A#2/A#3/A#4/A#5/A#6/A
4608 atoms, 5142 bonds, 228 residues, 6 models selected
> ui tool show "Color Actions"
> color sel pale green
> undo
> select clear
> select #1/A#2/A#3/A#4/A#5/A#6/A
4608 atoms, 5142 bonds, 228 residues, 6 models selected
> surface (#!1-6 & sel)
> ui tool show "Color Actions"
> color sel light green
> color sel light coral
> color sel aquamarine
> color sel pale turquoise
> color sel silver
> color sel lavender
> color sel plum
> color sel wheat
[Repeated 1 time(s)]
> color sel linen
> color sel lavender blush
> color sel misty rose
> color sel pink
> color sel peach puff
> color sel lemon chiffon
> color sel light yellow
> color sel lemon chiffon
> select clear
> save C:/Users/Usuario/Desktop/Thesis/cell_images/Go.cxs
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> hide #!1 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/10_Active_beta.png width
> 2241 height 1154 supersample 3 transparentBackground true
> show #!4 models
> hide #!5 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/9_I4_inside.png width 2241
> height 1154 supersample 3 transparentBackground true
> show #!3 models
> hide #!4 models
> select #3/E
10585 atoms, 10754 bonds, 1342 residues, 1 model selected
> surface (#!3 & sel)
> transparency (#!3 & sel) 0
> color (#!3 & sel) light gray
> transparency (#!3 & sel) 50
> select clear
> select #3/F
10556 atoms, 10515 bonds, 148 pseudobonds, 2634 residues, 2 models selected
> surface (#!3 & sel)
> graphics silhouettes false
> ui tool show "Color Actions"
> color sel ghost white
> select clear
> lighting soft
> ui tool show "Model Panel"
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> graphics silhouettes true
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/8_I3_inside.png width 2241
> height 1154 supersample 3 transparentBackground true
> show #!2 models
> hide #!3 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/7_I2_inside.png width 2241
> height 1154 supersample 3 transparentBackground true
> show #!1 models
> hide #!2 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/6_I1_inside.png width 2241
> height 1154 supersample 3 transparentBackground true
> show #!6 models
> hide #!1 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/5_Recruited_beta.png width
> 2241 height 1154 supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> ui tool show "Side View"
[Repeated 1 time(s)]
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/6_I1_inside.png width
> 2241 height 1154 supersample 3 transparentBackground true
> show #!2 models
> hide #!2 models
> select #1/H:3419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/H:3419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/F:2156@CD1
1 atom, 1 residue, 1 model selected
> select #1/F:2156@CD1
1 atom, 1 residue, 1 model selected
> select #1/H:3419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/H:3418
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/H:3417
27 atoms, 25 bonds, 3 residues, 1 model selected
> select subtract #1/H:3417
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/H:3416
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #1/H:3417
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add #1/H:3415
42 atoms, 38 bonds, 5 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/6_I1_inside.png width
> 1241 height 639 supersample 3
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/6_I1_inside.png width
> 2241 height 1154 supersample 3 transparentBackground true
> show #!2 models
> select #2/H:3421
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> select #2/H:3420
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/H:3421
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/H:3421
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> hide #!2 models
> show #!4 models
> select #1/H:3420
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> select clear
> show #!2 models
> hide #!1 models
> hide #!4 models
> select #2/H:3420
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> select clear
> select #2/H:3419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:3419
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/H:3418
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #2/H:3417
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add #2/H:3415
34 atoms, 31 bonds, 4 residues, 1 model selected
> select subtract #2/H:3415
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add #2/H:3415
34 atoms, 31 bonds, 4 residues, 1 model selected
> select subtract #2/H:3415
27 atoms, 25 bonds, 3 residues, 1 model selected
> select add #2/H:3415
34 atoms, 31 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/7_I2_inside.png width
> 2241 height 1154 supersample 3 transparentBackground true
> show #!1 models
> hide #!2 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/6_I1_inside.png width
> 2241 height 1154 supersample 3 transparentBackground true
> show #!3 models
> select #3/H:3350@ND2
1 atom, 1 residue, 1 model selected
> select #3/H:3351@N
1 atom, 1 residue, 1 model selected
> select #3/H:3350@CA
1 atom, 1 residue, 1 model selected
> select #3/H:3350@ND2
1 atom, 1 residue, 1 model selected
> select #3/H:3350@CA
1 atom, 1 residue, 1 model selected
> hide #!1 models
> select clear
> select #3/H:3350@CB
1 atom, 1 residue, 1 model selected
> select #3/H
1295 atoms, 1326 bonds, 162 residues, 1 model selected
> surface hidePatches (#!3 & sel)
> select clear
> select #3/H:3351
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/H:3351
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #3/H:3352
14 atoms, 12 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/8_I3_inside.png width
> 2241 height 1154 supersample 3 transparentBackground true
> show #!5 models
> hide #!3 models
> select #5/H:93
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
[Repeated 1 time(s)]
> select clear
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/10_Active_beta.png
> width 2241 height 1154 supersample 3 transparentBackground true
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/View_1_Cell.cxs
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting full
[Repeated 3 time(s)]
> lighting soft
> lighting full
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> show #!6 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/all_in_one.png width
> 2241 height 1154 supersample 3 transparentBackground true
> save C:/Users/Usuario/Desktop/Thesis/cell_images/view1/View_1_Cell.cxs
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> open C:/Users/Usuario/Desktop/Thesis/cell_images/view1/traj.part0001.xtc
Replaced existing frames of opsPEC_RfaH_recruited_SMOG.pdb #6 with 2135 new
frames
> movie record
> movie encode C:\Users\Usuario/Desktop/movie.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> cd C:/Users/Usuario/Desktop/Thesis/cell_images/view1
Current working directory is:
C:\Users\Usuario\Desktop\Thesis\cell_images\view1
> cd C:/Users/Usuario/Desktop/Thesis/cell_images/view1
Current working directory is:
C:\Users\Usuario\Desktop\Thesis\cell_images\view1
> cd C:\Users\Usuario\Desktop\Thesis\cell_images\view1\
Current working directory is:
C:\Users\Usuario\Desktop\Thesis\cell_images\view1
> cd C:\Users\Usuario\Desktop\Thesis\cell_images\view1\
Current working directory is:
C:\Users\Usuario\Desktop\Thesis\cell_images\view1
> ui windowfill toggle
[Repeated 1 time(s)]
> chimerax script.py
Unknown command: chimerax script.py
> cd C:/Users/Usuario/Desktop/Thesis/cell_images/view1
Current working directory is:
C:\Users\Usuario\Desktop\Thesis\cell_images\view1
> chimerax script.py
Unknown command: chimerax script.py
> chimeraX script.py
Unknown command: chimeraX script.py
> chimeraX script.py
Unknown command: chimeraX script.py
> C:\Program Files\ChimeraX\bin\ChimeraX --nogui --script script.py
Unknown command: C:\Program Files\ChimeraX\bin\ChimeraX --nogui --script
script.py
> C:\Program Files\ChimeraX\bin\ChimeraX --nogui --script
> C:\Users\Usuario\Desktop\Thesis\cell_images\script.py
Unknown command: C:\Program Files\ChimeraX\bin\ChimeraX --nogui --script
C:\Users\Usuario\Desktop\Thesis\cell_images\script.py
> mdmovie read
> "C:\Users\Usuario\Desktop\Thesis\cell_images\view1\trayectoria.xtc"
Unknown command: mdmovie read
"C:\Users\Usuario\Desktop\Thesis\cell_images\view1\trayectoria.xtc"
> mdmovie read
> C:\Users\Usuario\Desktop\Thesis\cell_images\view1\trayectoria.xtc
Unknown command: mdmovie read
C:\Users\Usuario\Desktop\Thesis\cell_images\view1\trayectoria.xtc
> mdmovie read
> "C:\Users\Usuario\Desktop\Thesis\cell_images\view1\traj.part0001.xtc"
Unknown command: mdmovie read
"C:\Users\Usuario\Desktop\Thesis\cell_images\view1\traj.part0001.xtc"
> mdmovie read
> C:\Users\Usuario\Desktop\Thesis\cell_images\view1\traj.part0001.xtc
Unknown command: mdmovie read
C:\Users\Usuario\Desktop\Thesis\cell_images\view1\traj.part0001.xtc
> mdmovie read
> C:\Users\Usuario\Desktop\Thesis\cell_images\view1\traj.part0001.xtc
Unknown command: mdmovie read
C:\Users\Usuario\Desktop\Thesis\cell_images\view1\traj.part0001.xtc
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> save
> C:/Users/Usuario/Desktop/Thesis/cell_images/view1/View_1_Cell_previo_a_movie.cxs
——— End of log from Fri Mar 31 12:22:44 2023 ———
opened ChimeraX session
> open trajectory.xtc
Replaced existing frames of opsPEC_RfaH_recruited_SMOG.pdb #6 with 2135 new
frames
> movie record
> smoothlines 5 fps 30 speed 1 ; movie encode
> /home/usuario/Desktop/movie_cell.mp4
Missing or invalid "models" argument: invalid surfaces specifier
> traj #0 movie record ; smooth 5 fps 30 speed 1 ; movie encode
> /home/usuario/Desktop/movie_cell.mp4
Unknown command: traj #0 movie record ; smooth 5 fps 30 speed 1 ; movie encode
/home/usuario/Desktop/movie_cell.mp4
> movie record
Already recording a movie
> movie encode /home/usuario/Desktop/movie.mp4 framerate 25.0
Movie encoding failed because no images were recorded.
> movie record
> movie record
Already recording a movie
> ui tool show "Selection Inspector"
> ui tool show "Molecular Dynamics Viewer"
Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
Chain information for structure #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 368, in thread_safe
func(*args, **kw)
File "/home/usuario/.local/share/ChimeraX/1.6/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme
self.openFile()
File "/home/usuario/.local/share/ChimeraX/1.6/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 234, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]
IndexError: list index out of range
IndexError: list index out of range
File "/home/usuario/.local/share/ChimeraX/1.6/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 234, in openFile
self.atomStruct.atoms.coords = self.atomLocation[0]
See log for complete Python traceback.
OpenGL version: 4.5 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa DRI Intel(R) HD Graphics 4400 (HSW GT2)
OpenGL vendor: Intel Open Source Technology Center
Python: 3.9.11
Locale: es_CL.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: ASUSTeK COMPUTER INC.
Model: X455LD
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i7-4510U CPU @ 2.00GHz
Cache Size: 4096 KB
Memory:
total used free shared buff/cache available
Mem: 7.6Gi 5.2Gi 281Mi 373Mi 2.1Gi 1.8Gi
Swap: 2.0Gi 1.9Gi 74Mi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Haswell-ULT Integrated Graphics Controller [8086:0a16] (rev 0b)
Subsystem: ASUSTeK Computer Inc. Haswell-ULT Integrated Graphics Controller [1043:170d]
Kernel driver in use: i915
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
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: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202303310103
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
ChimeraX-PDBBio: 1.0
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
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: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
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: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.1.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MD Viewer: self.atomLocation[0]: list index out of range |
comment:2 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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Not a multi-model PDB file