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Opened 8 months ago
Last modified 8 months ago
#17360 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs format session
Not registering illegal selector name "5_5a_crystal"
Log from Thu Apr 10 14:34:42 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
Not registering illegal selector name "5_5a_crystal"
Log from Wed Apr 9 09:24:04 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
Not registering illegal selector name "5_5a_crystal"
Log from Fri Apr 4 15:35:46 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/alexandrakaragiaridi/Desktop/MolBC_chains_renamed.pdb
Chain information for MolBC_chains_renamed.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> set bgColor white
> select /B:6-330
2347 atoms, 2398 bonds, 2 pseudobonds, 308 residues, 2 models selected
> color #1 #929292ff
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT/MolBC_WT_final_structure.pdb
Chain information for MolBC_WT_final_structure.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> select #2/B:7-328
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!2 & sel) blue
> select #2/C:6-328
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!2 & sel) cornflower blue
> select #2/D:2-252
1977 atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
> color (#!2 & sel) purple
> select #2/E:2-252
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> select add #2
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #2
Nothing selected
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure.pdb, chain C (#2) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> select /B:6-330
4581 atoms, 4680 bonds, 4 pseudobonds, 602 residues, 4 models selected
> select /B:6-330
4581 atoms, 4680 bonds, 4 pseudobonds, 602 residues, 4 models selected
> select /B:6-330
4581 atoms, 4680 bonds, 4 pseudobonds, 602 residues, 4 models selected
> select add #2
10766 atoms, 10989 bonds, 10 pseudobonds, 1392 residues, 4 models selected
> select subtract #2
2347 atoms, 2398 bonds, 2 pseudobonds, 308 residues, 2 models selected
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> select /B:6-330
4581 atoms, 4680 bonds, 4 pseudobonds, 602 residues, 4 models selected
> select /B:6-330
4581 atoms, 4680 bonds, 4 pseudobonds, 602 residues, 4 models selected
> select add #1
11483 atoms, 11025 bonds, 7 pseudobonds, 2083 residues, 4 models selected
> select subtract #1
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> select add #2
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #2
Nothing selected
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> hide #!2 models
> open /Users/alexandrakaragiaridi/Desktop/MolBC_WT.cif
Summary of feedback from opening
/Users/alexandrakaragiaridi/Desktop/MolBC_WT.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for MolBC_WT.cif #3
---
Chain | Description
Aa | No description available
Ab | No description available
Ba | No description available
Bb | No description available
> close #3
> open /Users/alexandrakaragiaridi/Desktop/MolBC_WT.cif
Summary of feedback from opening
/Users/alexandrakaragiaridi/Desktop/MolBC_WT.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for MolBC_WT.cif #3
---
Chain | Description
Aa | No description available
Ab | No description available
Ba | No description available
Bb | No description available
> close #3
> show #!2 models
> hide #!2 models
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_final_structure_chains_renamed.pdb
Chain information for MolBC_WT_final_structure_chains_renamed.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> select #3/B:6-328
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!3 & sel) blue
> select #3/C:7-328
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!3 & sel) cornflower blue
> select #3/D:2-252
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> color (#!3 & sel) hot pink
> color (#!3 & sel) purple
> select #3/E:2-252
1977 atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> matchmaker #1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> ui mousemode right zoom
> close #2
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
> ui mousemode right zoom
> open /Users/alexandrakaragiaridi/Desktop/MolBC_WT.cif
Summary of feedback from opening
/Users/alexandrakaragiaridi/Desktop/MolBC_WT.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for MolBC_WT.cif #2
---
Chain | Description
Aa | No description available
Ab | No description available
Ba | No description available
Bb | No description available
> close #2
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
Alignment identifier is 1/C
> select #3/C
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
Alignment identifier is 3/C
> select up
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select up
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> ~select
Nothing selected
> matchmaker #1/C:5-330 to #3/C:7-328
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 1410.2
RMSD between 279 pruned atom pairs is 0.889 angstroms; (across all 291 pairs:
1.859)
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie2.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie2.mp4
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
Alignment identifier is 1/B
> select #3/B
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
Alignment identifier is 3/B
> ~select
Nothing selected
> matchmaker #1/B:6-330 to #3/C:6-328
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1402
RMSD between 288 pruned atom pairs is 0.895 angstroms; (across all 294 pairs:
1.078)
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie3.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie3.mp4
> matchmaker #1/B:6-330 to #3/B:6-328
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> select #1/B:53
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:53-86
249 atoms, 250 bonds, 34 residues, 1 model selected
> select #3/B:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:54-86
242 atoms, 243 bonds, 33 residues, 1 model selected
> matchmaker #1/B:53-86 to #3/B:54-86
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 170
RMSD between 33 pruned atom pairs is 0.613 angstroms; (across all 33 pairs:
0.613)
> ~select
Nothing selected
> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie4.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie4.mp4
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
Alignment identifier is 1/C
> select #3/C
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
Alignment identifier is 3/C
> select #1/C:63
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:63-86
162 atoms, 162 bonds, 24 residues, 1 model selected
> select #3/C:63
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:63-87
173 atoms, 174 bonds, 25 residues, 1 model selected
> matchmaker #1/C:63-86 to #3/C:63-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 123.7
RMSD between 24 pruned atom pairs is 0.263 angstroms; (across all 24 pairs:
0.263)
> ~select
Nothing selected
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
> matchmaker #1/B,C to #3/B,C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> select #1/B,C
4909 atoms, 4703 bonds, 4 pseudobonds, 912 residues, 2 models selected
> name WT_TMD_crystal /B,C
> ~select
Nothing selected
> select WT_TMD_crystal
9466 atoms, 9359 bonds, 8 pseudobonds, 1510 residues, 4 models selected
> ~select
Nothing selected
> select #3/B,C
4557 atoms, 4656 bonds, 4 pseudobonds, 598 residues, 2 models selected
> name WT_TMD_cryo /B,C
> ~select
Nothing selected
> select WT_TMD_crystal
9466 atoms, 9359 bonds, 8 pseudobonds, 1510 residues, 4 models selected
> select #1/B,C
4909 atoms, 4703 bonds, 4 pseudobonds, 912 residues, 2 models selected
> name WT_TMD_crystal #1/B,C
> name WT_TMD_cryo #3/B,C
> ~select
Nothing selected
> select WT_TMD_crystal
4909 atoms, 4703 bonds, 4 pseudobonds, 912 residues, 2 models selected
> select WT_TMD_cryo
4557 atoms, 4656 bonds, 4 pseudobonds, 598 residues, 2 models selected
> ~select
Nothing selected
> matchmaker WT_TMD_crystal to WT_TMD_cryo
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> matchmaker #1/D to #3/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain D (#3) with
MolBC_chains_renamed.pdb, chain D (#1), sequence alignment score = 1119.7
RMSD between 236 pruned atom pairs is 0.864 angstroms; (across all 238 pairs:
1.082)
> ui mousemode right "rotate selected models"
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie2.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie2.mp4
> matchmaker #1/E to #3/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain E (#3) with
MolBC_chains_renamed.pdb, chain E (#1), sequence alignment score = 1188
RMSD between 242 pruned atom pairs is 0.927 angstroms; (across all 244 pairs:
0.967)
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie3.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie3.mp4
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_final_structure.pdb
Chain information for MolBC_WT_final_structure.pdb #2
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> ui tool show "Change Chain IDs"
> changechains C B
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/5/)
> hide #!2 models
> show #!1 models
> show #!3 models
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
Alignment identifier is 1/B
> select #3/B
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
Alignment identifier is 3/B
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> matchmaker #1/B:6-330, C:5-330 to #3/B:6-328, C:7-328
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> matchmaker #1/B:6-330 \+ C:5-330 to #3/B:6-328 + C:7-328
Expected a keyword
> close #2
> hide #!1 models
> ui mousemode right zoom
> select #3/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:147-171
190 atoms, 191 bonds, 25 residues, 1 model selected
> select #3/C:147-171,177-185
268 atoms, 272 bonds, 34 residues, 1 model selected
> select #3/C:7
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:7-146
840 atoms, 857 bonds, 2 pseudobonds, 112 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/C:186-187
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/C:186-328
1087 atoms, 1111 bonds, 143 residues, 1 model selected
> cartoon hide sel
> select #3/B:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:149-171
174 atoms, 175 bonds, 23 residues, 1 model selected
> select #3/B:141
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:130-141
95 atoms, 97 bonds, 12 residues, 1 model selected
> select #3/B:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:6-148
945 atoms, 965 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/B:187-188
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #3/B:187-324
1045 atoms, 1068 bonds, 138 residues, 1 model selected
> cartoon hide sel
> select #3/B:328
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/B:325-328
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B:325-328
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B:325-328
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B:325-328
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B:325-328
34 atoms, 34 bonds, 4 residues, 1 model selected
> cartoon hide sel
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> select #3/D,E
3862 atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
> cartoon hide (#!3 & sel)
> ui mousemode right "translate selected models"
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!1 models
> select #1/D,E
4340 atoms, 4040 bonds, 1 pseudobond, 877 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/C:148-149
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/C:148-170
174 atoms, 175 bonds, 23 residues, 1 model selected
> hide #!3 models
> select #1/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:5-147
855 atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/C:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:186-330
1104 atoms, 1128 bonds, 145 residues, 1 model selected
> cartoon hide sel
> select #1/B:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:147-170
182 atoms, 183 bonds, 24 residues, 1 model selected
> select #1/B:141-146
15 atoms, 13 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #1/B:6-146
936 atoms, 956 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/B:187
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:187-330
1096 atoms, 1120 bonds, 144 residues, 1 model selected
> cartoon hide sel
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> ~select
Nothing selected
> select #1/B:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> select #1/C:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #1/B:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> select #1/B:147-186, C:148-185
315 atoms, 320 bonds, 40 residues, 1 model selected
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> transparency 0
> hide #!3 models
> ui mousemode right select
Drag select of 78 residues
> name 5_5a_crystal #1/sel
Not registering illegal selector name "5_5a_crystal"
> name TM5_5a_crystal #1/sel
> ~select
Nothing selected
> select TM5_5a_crystal
Nothing selected
Drag select of 78 residues
> ui tool show Matchmaker
> show #!3 models
Drag select of 155 residues
> ui tool show Matchmaker
> matchmaker #!3 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_chains_renamed.pdb, chain B (#1) with
MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3), sequence alignment
score = 193.8
RMSD between 39 pruned atom pairs is 0.569 angstroms; (across all 39 pairs:
0.569)
> matchmaker #!3 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_chains_renamed.pdb, chain B (#1) with
MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3), sequence alignment
score = 193.8
RMSD between 39 pruned atom pairs is 0.569 angstroms; (across all 39 pairs:
0.569)
> ~select
Nothing selected
> ui mousemode right zoom
> cartoon
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
> select #1/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:5-147
855 atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
> ~select
Nothing selected
> select #1/C:5
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:5-147
855 atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/C:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:171-330
1229 atoms, 1257 bonds, 160 residues, 1 model selected
> cartoon hide sel
> select #3/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:7-146
840 atoms, 857 bonds, 2 pseudobonds, 112 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/C:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:172-328
1204 atoms, 1232 bonds, 157 residues, 1 model selected
> cartoon hide sel
> select #1/B:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:6-146
936 atoms, 956 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:171-330
1229 atoms, 1257 bonds, 160 residues, 1 model selected
> cartoon hide sel
> select #3/B:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:6-148
945 atoms, 965 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/B:172-328
1204 atoms, 1232 bonds, 157 residues, 1 model selected
> cartoon hide sel
> select #1/D,E
4340 atoms, 4040 bonds, 1 pseudobond, 877 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #3/D,E
3862 atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #!1 models
> open "/Users/alexandrakaragiaridi/Dropbox/Type II PDB structures/1l7v -
> BtuCD.pdb"
1l7v - BtuCD.pdb title:
Bacterial abc transporter involved In B12 uptake [more info...]
Chain information for 1l7v - BtuCD.pdb #2
---
Chain | Description | UniProt
A B | vitamin B12 transport system permease protein btuc | BTUC_ECOLI 1-326
C D | vitamin B12-transporting atpase | BTUD_ECOLI 1-249
Non-standard residues in 1l7v - BtuCD.pdb #2
---
V4O — cyclo-tetrametavanadate
> hide #!3 models
> view
> select #2/B:1-324
2441 atoms, 2495 bonds, 324 residues, 1 model selected
Alignment identifier is 2/B
> ~select
Nothing selected
> select
> #2/B:2-33,45-81,92-108,113-139,141-168,171-180,187-205,207-224,227-251,258-267,271-297,304-324
2064 atoms, 2097 bonds, 271 residues, 1 model selected
> select #2/B:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:328
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/B:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,26.763,0,1,0,7.3901,0,0,1,-31.543
> ui mousemode right zoom
> hide #2 models
> select add #2
8410 atoms, 8582 bonds, 1112 residues, 1 model selected
> select subtract #2
Nothing selected
> show #!3 models
> view
> select #3/B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/B:172-186
125 atoms, 128 bonds, 15 residues, 1 model selected
> cartoon sel
> ui mousemode right "translate selected models"
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> select #3/B:172-186
125 atoms, 128 bonds, 15 residues, 1 model selected
> select #3/B:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:186-187
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/B:172-186
125 atoms, 128 bonds, 15 residues, 1 model selected
> cartoon hide sel
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> ui mousemode right zoom
[Repeated 1 time(s)]
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]Exactly two atoms must be selected!
> ui mousemode right select
> select #3/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:171
8 atoms, 7 bonds, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #3/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/C:171
16 atoms, 14 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> distance #3/B:171 #3/C:171 color black
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects
> distance B:171 C:171 color black
Missing or invalid "objects" argument: only initial part "B" of atom specifier
valid
> ui tool show Distances
Exactly two atoms must be selected!
> show sel atoms
Exactly two atoms must be selected!
> distance /B:171@ca /C:171@ca
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 6 atoms and 0
measurable objects
> distance /B:171@ca /C:171@ca
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 6 atoms and 0
measurable objects
> distance #3/B:171@ca #3/C:171@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 171 CA
and /C ILE 171 CA: 23.254Å
> label height 1
> label height 2
> label height 1.5
> distance #3/B:169@ca #3/C:169@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B GLN 169 CA
and /C GLN 169 CA: 15.005Å
> label height 1.5
> hide sel atoms
> ~select
Nothing selected
> distance #3/B:167@ca #3/C:167@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B LEU 167 CA
and /C LEU 167 CA: 22.657Å
> label height 1.5
> distance #3/B:165@ca #3/C:165@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B VAL 165 CA
and /C VAL 165 CA: 18.432Å
> label height 1.5
> distance #3/B:163@ca #3/C:163@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ALA 163 CA
and /C ALA 163 CA: 20.352Å
> label height 1.5
> distance #3/B:161@ca #3/C:161@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B PHE 161 CA
and /C PHE 161 CA: 22.692Å
> label height 1.5
> distance #3/B:159@ca #3/C:159@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B GLY 159 CA
and /C GLY 159 CA: 18.050Å
> label height 1.5
> distance #3/B:157@ca #3/C:157@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B LEU 157 CA
and /C LEU 157 CA: 25.168Å
> label height 1.5
> distance #3/B:155@ca #3/C:155@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B MET 155 CA
and /C MET 155 CA: 16.815Å
> label height 1.5
> distance #3/B:153@ca #3/C:153@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 153 CA
and /C ILE 153 CA: 26.245Å
> label height 1.5
> distance #3/B:151@ca #3/C:151@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 151 CA
and /C ILE 151 CA: 18.493Å
> label height 1.5
> distance #3/B:149@ca #3/C:149@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B MET 149 CA
and /C MET 149 CA: 25.488Å
> label height 1.5
> ui mousemode right "move label"
> ui mousemode right zoom
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #!3 models
> hide #!4 models
> hide #4.1 models
> show #!1 models
> show #!3 models
> ui mousemode right "translate selected models"
> hide #!3 models
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> cartoon #1,3
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> matchmaker #1/B to #3/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #3/B
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> matchmaker #1/B:53-86 to #3/B:53-86
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 171
RMSD between 34 pruned atom pairs is 0.653 angstroms; (across all 34 pairs:
0.653)
> ~select
Nothing selected
> matchmaker #1/C to #3/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 1410.2
RMSD between 279 pruned atom pairs is 0.889 angstroms; (across all 291 pairs:
1.859)
> matchmaker #1/C:63-86 to #3/C:63-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 123.7
RMSD between 24 pruned atom pairs is 0.263 angstroms; (across all 24 pairs:
0.263)
> matchmaker #1/D to #3/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain D (#3) with
MolBC_chains_renamed.pdb, chain D (#1), sequence alignment score = 1119.7
RMSD between 236 pruned atom pairs is 0.864 angstroms; (across all 238 pairs:
1.082)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> select #1/D
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> matchmaker #1/D to #3/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain D (#3) with
MolBC_chains_renamed.pdb, chain D (#1), sequence alignment score = 1119.7
RMSD between 236 pruned atom pairs is 0.864 angstroms; (across all 238 pairs:
1.082)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> select #1/D
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> select #1/E
2175 atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
> matchmaker #1/C:63-86 to #3/C:63-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 123.7
RMSD between 24 pruned atom pairs is 0.263 angstroms; (across all 24 pairs:
0.263)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> select #1/D
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> select #1/E
2175 atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
> matchmaker #1/C to #3/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 1410.2
RMSD between 279 pruned atom pairs is 0.889 angstroms; (across all 291 pairs:
1.859)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> select #1/D
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> select #1/E
2175 atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
> matchmaker #1/B:53-86 to #3/B:53-86
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 171
RMSD between 34 pruned atom pairs is 0.653 angstroms; (across all 34 pairs:
0.653)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> select #1/D
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> matchmaker #1/B to #3/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 1451.5
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> select #1/D
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> matchmaker #1/E to #3/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain E (#3) with
MolBC_chains_renamed.pdb, chain E (#1), sequence alignment score = 1188
RMSD between 242 pruned atom pairs is 0.927 angstroms; (across all 244 pairs:
0.967)
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> select #3/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:147-149
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #3/B:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:149-152
32 atoms, 31 bonds, 4 residues, 1 model selected
> select #1/C:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #3/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:147-150
32 atoms, 31 bonds, 4 residues, 1 model selected
> ui mousemode right select
> select #1/C:148-149
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #3/C:147-185
307 atoms, 312 bonds, 39 residues, 1 model selected
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #3/C:147-185
307 atoms, 312 bonds, 39 residues, 1 model selected
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #3/C:147-185
307 atoms, 312 bonds, 39 residues, 1 model selected
> select #1/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:5-147
855 atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/C:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:186-330
1104 atoms, 1128 bonds, 145 residues, 1 model selected
> cartoon hide sel
> select #3/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:7-146
840 atoms, 857 bonds, 2 pseudobonds, 112 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/C:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:186-328
1087 atoms, 1111 bonds, 143 residues, 1 model selected
> cartoon hide sel
> select #1/B:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:6-146
936 atoms, 956 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/B:187
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:187-330
1096 atoms, 1120 bonds, 144 residues, 1 model selected
> cartoon hide sel
> select #3/B:145-146
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B:142-146
36 atoms, 35 bonds, 1 pseudobond, 4 residues, 2 models selected
> select #3/B:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:6-148
945 atoms, 965 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/B:328
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/B:187-328
1079 atoms, 1103 bonds, 142 residues, 1 model selected
> cartoon hide sel
> select #1/D,E
4340 atoms, 4040 bonds, 1 pseudobond, 877 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #3/D,E
3862 atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select add #3
8419 atoms, 8591 bonds, 20 pseudobonds, 1084 residues, 3 models selected
> select subtract #3
Nothing selected
Drag select of 155 residues
> matchmaker #!3 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_chains_renamed.pdb, chain B (#1) with
MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3), sequence alignment
score = 193.8
RMSD between 39 pruned atom pairs is 0.569 angstroms; (across all 39 pairs:
0.569)
> cartoon sel
> ~select
Nothing selected
> cartoon #1,3
> ui mousemode right "translate selected models"
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select #3/B:328
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/B:187-328
1079 atoms, 1103 bonds, 142 residues, 1 model selected
> ~select
Nothing selected
> ui tool show Matchmaker
> hide #!3 models
> select #1/B:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> select #1/C:148-330
1403 atoms, 1433 bonds, 183 residues, 1 model selected
> select #1/C:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #1/B:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #1/B:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> select #1/B:147-186 & #1/C:148-185
Nothing selected
> select #1/B:147-186 & /C:148-185
Nothing selected
> select #1/B:147-186, C:148-185
315 atoms, 320 bonds, 40 residues, 1 model selected
> select #1/B:147-186, #1/C:148-185
Expected an objects specifier or a keyword
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> show #!3 models
> ~select
Nothing selected
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> matchmaker #1/E to #3/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain E (#3) with
MolBC_chains_renamed.pdb, chain E (#1), sequence alignment score = 1188
RMSD between 242 pruned atom pairs is 0.927 angstroms; (across all 244 pairs:
0.967)
> ~select
Nothing selected
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> ~SEL
Unknown command: ~SEL
> ~select
Nothing selected
> matchmaker #1/B:147-186 to #3/B:149-186
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 189.9
RMSD between 38 pruned atom pairs is 0.500 angstroms; (across all 38 pairs:
0.500)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> select
26078 atoms, 25916 bonds, 25 pseudobonds, 3985 residues, 7 models selected
> ~select
Nothing selected
> matchmaker #1/C:148-185 to #3/C:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain C (#1), sequence alignment score = 189.2
RMSD between 38 pruned atom pairs is 0.592 angstroms; (across all 38 pairs:
0.592)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> ~select
Nothing selected
> ui mousemode right select
Drag select of 409 residues, 4 pseudobonds
> ~select
Nothing selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select
26078 atoms, 25916 bonds, 25 pseudobonds, 3985 residues, 7 models selected
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> ~select
Nothing selected
> align
Missing or invalid "atoms" argument: empty atom specifier
> ui tool show Matchmaker
> matchmaker #!3 & sel to #1 & sel showAlignment true
No 'to' model specified
> matchmaker #!3 & sel to #1 & sel showAlignment true
No 'to' model specified
> matchmaker #!3 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_chains_renamed.pdb, chain B (#1) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 1451.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: MolBC_chains_renamed.pdb #1/B,
MolBC_WT_final_structure_chains_renamed.pdb #3/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 296 pruned atom pairs is 0.913 angstroms; (across all 301 pairs:
1.077)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> ~select
Nothing selected
> select TM5_5a_crystal
Nothing selected
> hide #!3 models
> select #1/B:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:147-150
32 atoms, 31 bonds, 4 residues, 1 model selected
> select #1/B:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> ui mousemode right select
> select #1/C:148-185
299 atoms, 304 bonds, 38 residues, 1 model selected
> select #1/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:5-147
855 atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/C:171-172
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:171-330
1229 atoms, 1257 bonds, 160 residues, 1 model selected
> cartoon hide sel
> select #1/B:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:6-146
936 atoms, 956 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:171-330
1229 atoms, 1257 bonds, 160 residues, 1 model selected
> cartoon hide sel
Drag select of 47 residues
> select up
2828 atoms, 2888 bonds, 369 residues, 1 model selected
> select up
2854 atoms, 2913 bonds, 372 residues, 1 model selected
> select up
4135 atoms, 4226 bonds, 546 residues, 1 model selected
> select up
4283 atoms, 4375 bonds, 565 residues, 1 model selected
> select up
4605 atoms, 4703 bonds, 608 residues, 1 model selected
> select down
4283 atoms, 4375 bonds, 565 residues, 1 model selected
> select down
4135 atoms, 4226 bonds, 546 residues, 1 model selected
> select down
2854 atoms, 2913 bonds, 372 residues, 1 model selected
> select down
2828 atoms, 2888 bonds, 369 residues, 1 model selected
> select down
356 atoms, 47 residues, 1 model selected
> select down
356 atoms, 47 residues, 1 model selected
> select down
356 atoms, 47 residues, 1 model selected
> select down
356 atoms, 47 residues, 1 model selected
> ~select
Nothing selected
Drag select of 47 residues
> select down
356 atoms, 47 residues, 1 model selected
> select up
2828 atoms, 2888 bonds, 369 residues, 1 model selected
> select down
356 atoms, 47 residues, 1 model selected
> ~select
Nothing selected
Drag select of 47 residues
> name 5_5a_crystal #1/sel
Not registering illegal selector name "5_5a_crystal"
> name TM5_5a_crystal_real #1/sel
> ~select
Nothing selected
> select TM5_5a_crystal_real
Nothing selected
Drag select of 47 residues
> name TM5_5a_crystal_real #1
> ~select
Nothing selected
> select TM5_5a_crystal_real
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> ~select
Nothing selected
> show #!3 models
> select #3/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:7-146
840 atoms, 857 bonds, 2 pseudobonds, 112 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/C:186-187
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/C:186-328
1087 atoms, 1111 bonds, 143 residues, 1 model selected
> cartoon hide sel
> select #3/C:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:172-185
117 atoms, 120 bonds, 14 residues, 1 model selected
> cartoon hide sel
> select #3/B:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:6-148
945 atoms, 965 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/B:171-172
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/B:172-328
1204 atoms, 1232 bonds, 157 residues, 1 model selected
> cartoon hide sel
> ui tool show Matchmaker
> select add #3
8419 atoms, 8591 bonds, 20 pseudobonds, 1084 residues, 3 models selected
> select subtract #3
Nothing selected
> matchmaker #1/B,C:147-186 to #3/B,C:147-186
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain C (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 195.5
RMSD between 40 pruned atom pairs is 0.574 angstroms; (across all 40 pairs:
0.574)
> matchmaker #1/B:147-186 to #3/B:149-186
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3) with
MolBC_chains_renamed.pdb, chain B (#1), sequence alignment score = 189.9
RMSD between 38 pruned atom pairs is 0.500 angstroms; (across all 38 pairs:
0.500)
> ui mousemode right "translate selected models"
> select #1/D,E
4340 atoms, 4040 bonds, 1 pseudobond, 877 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #3/D,E
3862 atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select add #3
8419 atoms, 8591 bonds, 20 pseudobonds, 1084 residues, 3 models selected
> select subtract #3
Nothing selected
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> ~select
Nothing selected
> ui mousemode right zoom
> hide #!3 models
> show #!3 models
> hide #!1 models
> distance #3/B:172@ca #3/C:172@ca
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B SER 172 CA
and /C SER 172 CA: 18.960Å
> show #!4 models
> show #4.1 models
> show #!1 models
> hide #!4 models
> hide #4.1 models
> cartoon #1,3
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
> hide #!1 models
> show #!4 models
> show #4.1 models
> select #3/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:7-146
840 atoms, 857 bonds, 2 pseudobonds, 112 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/C:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:172-328
1204 atoms, 1232 bonds, 157 residues, 1 model selected
> cartoon hide sel
> select #3/B:328
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/B:172-328
1204 atoms, 1232 bonds, 157 residues, 1 model selected
> cartoon hide sel
> select #3/B:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:6-148
945 atoms, 965 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/D,E
3862 atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select add #3
8419 atoms, 8591 bonds, 21 pseudobonds, 1084 residues, 3 models selected
> select subtract #3
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #!4 models
> hide #4.1 models
> hide #!3 models
> show #!1 models
> select #1/C:329-330
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/C:171-330
1229 atoms, 1257 bonds, 160 residues, 1 model selected
> cartoon hide sel
> select #1/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:5-147
855 atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/B:330
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:171-330
1229 atoms, 1257 bonds, 160 residues, 1 model selected
> cartoon hide sel
> select #1/B:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:6-146
936 atoms, 956 bonds, 2 pseudobonds, 124 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/D,E
4340 atoms, 4040 bonds, 1 pseudobond, 877 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select add #1
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> hide #!3 models
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> ~select
Nothing selected
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> color (#!1 & sel) blue
> select #1/C
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> ~select
Nothing selected
> distance #1/B:171@ca #1/C:171@ca
Distance between MolBC_chains_renamed.pdb #1/B ILE 171 CA and /C ILE 171 CA:
22.605Å
> show #!4 models
> show #4.1 models
> hide #4.1 models
> hide #!4 models
> show #!3 models
> show #!4 models
> show #4.1 models
> hide #!4 models
> hide #4.1 models
> distance #1/B:171@ca #1/C:171@ca color black
Distance already exists; modify distance properties with 'distance style'
> distance #1/B:171@ca #1/C:171@ca color yellow
Distance already exists; modify distance properties with 'distance style'
> distance style
> ui tool show Distances
Exactly two atoms must be selected!
> ~distance #1/B:171@CA #1/C:171@CA
Exactly two atoms must be selected!
> distance #1/B:171@ca #1/C:171@ca color yellow
Distance between MolBC_chains_renamed.pdb #1/B ILE 171 CA and /C ILE 171 CA:
22.605Å
> show distance
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> close #4
> distance #1/B:171@ca #1/C:171@ca color black
Distance between MolBC_chains_renamed.pdb #1/B ILE 171 CA and /C ILE 171 CA:
22.605Å
> hide #!3 models
> select add #4
1 pseudobond, 2 models selected
> select subtract #4
Nothing selected
> view
> ui tool show Distances
Exactly two atoms must be selected!
> select
> #1/C:6-26,58-60,63-86,99-112,117-137,148-170,177-185,194-214,217-222,225-230,235-256,267-275,279-304,311-327
1674 atoms, 1695 bonds, 222 residues, 1 model selected
> select #1/C:5-147
855 atoms, 871 bonds, 2 pseudobonds, 117 residues, 2 models selected
> select #1/C:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #1/B:170
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:170
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/C:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> cartoon sel
> select #1/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> cartoon sel
> ~select
Nothing selected
> distance #1/B:169@ca #1/C:169@ca color black
Distance between MolBC_chains_renamed.pdb #1/B GLN 169 CA and /C GLN 169 CA:
14.324Å
> distance #1/B:167@ca #1/C:167@ca color black
Distance between MolBC_chains_renamed.pdb #1/B LEU 167 CA and /C LEU 167 CA:
21.854Å
> distance #1/B:165@ca #1/C:165@ca color black
Distance between MolBC_chains_renamed.pdb #1/B VAL 165 CA and /C VAL 165 CA:
17.548Å
> distance #1/B:163@ca #1/C:163@ca color black
Distance between MolBC_chains_renamed.pdb #1/B ALA 163 CA and /C ALA 163 CA:
19.665Å
> distance #1/B:161@ca #1/C:161@ca color black
Distance between MolBC_chains_renamed.pdb #1/B PHE 161 CA and /C PHE 161 CA:
22.059Å
> distance #1/B:159@ca #1/C:159@ca color black
Distance between MolBC_chains_renamed.pdb #1/B GLY 159 CA and /C GLY 159 CA:
17.961Å
> distance #1/B:157@ca #1/C:157@ca color black
Distance between MolBC_chains_renamed.pdb #1/B LEU 157 CA and /C LEU 157 CA:
24.684Å
> distance #1/B:155@ca #1/C:155@ca color black
Distance between MolBC_chains_renamed.pdb #1/B MET 155 CA and /C MET 155 CA:
16.572Å
> distance #1/B:153@ca #1/C:153@ca color black
Distance between MolBC_chains_renamed.pdb #1/B ILE 153 CA and /C ILE 153 CA:
25.521Å
> distance #1/B:151@ca #1/C:151@ca color black
Distance between MolBC_chains_renamed.pdb #1/B ILE 151 CA and /C ILE 151 CA:
17.659Å
> distance #1/B:149@ca #1/C:149@ca color black
Distance between MolBC_chains_renamed.pdb #1/B MET 149 CA and /C MET 149 CA:
24.266Å
> label height 1.5
[Repeated 1 time(s)]
> ui mousemode right "move label"
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!4 models
> hide #4.1 models
> show #!3 models
> color #1 #929292ff
> ui mousemode right zoom
> cartoon #1,3
> ui mousemode right "translate selected models"
> morph
Missing or invalid "structures" argument: empty atom specifier
> morph #3,1 frames 40
Computed 41 frame morph #5
> coordset #5 1,41
> morph #3,1 frames 60
Computed 61 frame morph #6
> coordset #6 1,61
> hide #!5 models
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> close #5
> hide #!6 models
> hide #4.1 models
> show #!1 models
> show #!3 models
> matchmaker #1/D to #3/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_final_structure_chains_renamed.pdb, chain D (#3) with
MolBC_chains_renamed.pdb, chain D (#1), sequence alignment score = 1119.7
RMSD between 236 pruned atom pairs is 0.864 angstroms; (across all 238 pairs:
1.082)
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> ~select
Nothing selected
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/alexandrakaragiaridi/Desktop/movie1.mp4
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie1.mp4
> hide #!1 models
> select #3/B,C
4557 atoms, 4656 bonds, 4 pseudobonds, 598 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select #3/D,E
3862 atoms, 3935 bonds, 4 pseudobonds, 486 residues, 2 models selected
Alignment identifier is 3/D
Alignment identifier is 3/E
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> ui mousemode right zoom
> view
> select #3/D:38-39
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/D:38-53
91 atoms, 89 bonds, 1 pseudobond, 13 residues, 2 models selected
> ~select
Nothing selected
> select #3/D:45
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/D:45
6 atoms, 5 bonds, 1 residue, 1 model selected
> ~select
Nothing selected
> select #3/D:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/D:129-133
31 atoms, 30 bonds, 5 residues, 1 model selected
> select #3/D:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/D:129-133
31 atoms, 30 bonds, 5 residues, 1 model selected
> select #3/E:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/E:129-133
31 atoms, 30 bonds, 5 residues, 1 model selected
> select add #3
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> select subtract #3
Nothing selected
> distance #3/D:45@ca #3/E:133@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/D SER 45 CA
and /E GLN 133 CA: 23.027Å
> show #4.1 models
> label height 1.5
> label height 2
> label height 4
> label height 3
[Repeated 1 time(s)]
> ui mousemode right "move label"
> select #3/D:45
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel black
> select #3/e:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel black
> ui mousemode right zoom
> select add #3
8419 atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 3 models selected
> select subtract #3
Nothing selected
> ui mousemode right "move label"
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!3 models
> show #!1 models
> hide #!4 models
> hide #4.1 models
> select #1/B,C
4909 atoms, 4703 bonds, 16 pseudobonds, 912 residues, 3 models selected
> cartoon hide (#!1 & sel)
> select #1/d
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> color sel purple
> select #1/e
2175 atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> distance #1/D:45@ca #1/E:133@ca color black
Distance between MolBC_chains_renamed.pdb #1/D SER 45 CA and /E GLN 133 CA:
22.019Å
> show #!4 models
> show #4.1 models
> label height 3
[Repeated 1 time(s)]
> select #1/e:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel black
> select #1/d:45
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel black
> ~select
Nothing selected
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #4.1 models
> hide #!4 models
> color #1 #929292ff
> hide #!1 models
> show #!3 models
> cartoon #3
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select #3/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> color (#!3 & sel) purple
> select #3/e
1977 atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> select #3
8419 atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 3 models selected
> show sel surfaces
> hide sel cartoons
> select add #4
8419 atoms, 8591 bonds, 22 pseudobonds, 1084 residues, 8 models selected
> select subtract #4
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 6 models selected
> ~select
Nothing selected
> ui mousemode right zoom
> ui tool show "Side View"
> hide #!3 models
> show #!1 models
> cartoon #1
> select #1/B
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> color (#!1 & sel) blue
> select #1/c
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select #1/d
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> color sel purple
> select #1/e
2175 atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> select #1
9249 atoms, 8743 bonds, 18 pseudobonds, 1789 residues, 3 models selected
> show sel surfaces
> hide sel cartoons
> ~select
Nothing selected
> hide #!1 models
> show #!3 models
> transparency #3 50
> transparency #3 70
> select #3/B,C
4557 atoms, 4656 bonds, 4 pseudobonds, 598 residues, 2 models selected
Alignment identifier is 3/B
Alignment identifier is 3/C
> ~select
Nothing selected
> select #3/B:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:149-171
174 atoms, 175 bonds, 23 residues, 1 model selected
> show sel cartoons
> select #3/C:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:147-171
190 atoms, 191 bonds, 25 residues, 1 model selected
> show sel cartoons
> ~select
Nothing selected
> distance #3/B:171@ca #3/C:171@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 171 CA
and /C ILE 171 CA: 23.254Å
> show #!4 models
> show #4.1 models
> distance #3/B:169@ca #3/C:169@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B GLN 169 CA
and /C GLN 169 CA: 15.005Å
> distance #3/B:167@ca #3/C:167@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B LEU 167 CA
and /C LEU 167 CA: 22.657Å
> distance #3/B:165@ca #3/C:165@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B VAL 165 CA
and /C VAL 165 CA: 18.432Å
> distance #3/B:163@ca #3/C:163@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ALA 163 CA
and /C ALA 163 CA: 20.352Å
> distance #3/B:161@ca #3/C:161@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B PHE 161 CA
and /C PHE 161 CA: 22.692Å
> distance #3/B:159@ca #3/C:159@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B GLY 159 CA
and /C GLY 159 CA: 18.050Å
> distance #3/B:157@ca #3/C:157@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B LEU 157 CA
and /C LEU 157 CA: 25.168Å
> distance #3/B:155@ca #3/C:155@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B MET 155 CA
and /C MET 155 CA: 16.815Å
> distance #3/B:153@ca #3/C:153@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 153 CA
and /C ILE 153 CA: 26.245Å
> distance #3/B:151@ca #3/C:151@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B ILE 151 CA
and /C ILE 151 CA: 18.493Å
> distance #3/B:149@ca #3/C:149@ca color black
Distance between MolBC_WT_final_structure_chains_renamed.pdb #3/B MET 149 CA
and /C MET 149 CA: 25.488Å
> label height 3
> label height 1.5
[Repeated 1 time(s)]
> transparency #3-4 0
> transparency #3-4 60
> label height 2.5
> label height 2
> ui mousemode right label
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right "move label"
> ui tool show Distances
[Repeated 1 time(s)]
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> select add #4
26 pseudobonds, 2 models selected
> select subtract #4
Nothing selected
> select add #4.1
1 model selected
> select add #4
26 pseudobonds, 2 models selected
> select subtract #4
Nothing selected
> ui mousemode right select
> select #3/D:246@CD
1 atom, 1 residue, 1 model selected
> select #3/D:246@CD
1 atom, 1 residue, 1 model selected
> ~select
Nothing selected
> ui tool show Distances
> ~distance #3/B:149@CA #3/C:149@CA
> ui mousemode right "move label"
> ~distance #3/B:151@CA #3/C:151@CA
> ~distance #3/B:153@CA #3/C:153@CA
> ~distance #3/B:155@CA #3/C:155@CA
> ~distance #3/B:157@CA #3/C:157@CA
> ~distance #3/B:159@CA #3/C:159@CA
> ~distance #3/B:161@CA #3/C:161@CA
> ~distance #3/B:163@CA #3/C:163@CA
> ~distance #3/B:165@CA #3/C:165@CA
> ~distance #3/B:167@CA #3/C:167@CA
> ~distance #3/B:169@CA #3/C:169@CA
> ~distance #3/B:171@CA #3/C:171@CA
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> hide #!3 models
> show #!1 models
> transparency #1,4 60
> select #1/b,c
4909 atoms, 4703 bonds, 16 pseudobonds, 912 residues, 3 models selected
Alignment identifier is 1/B
Alignment identifier is 1/C
> ~select
Nothing selected
> select #1/B:147-148
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/B:147-170
182 atoms, 183 bonds, 24 residues, 1 model selected
> show sel cartoons
> select #1/C:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:148-170
174 atoms, 175 bonds, 23 residues, 1 model selected
> show sel cartoons
> ~select
Nothing selected
> ui mousemode right "move label"
> color #4 black models
> ui tool show Distances
> ~distance #1/B:149@CA #1/C:149@CA
> distance #1/B:149@ca #1/C:149@ca color black
Distance between MolBC_chains_renamed.pdb #1/B MET 149 CA and /C MET 149 CA:
24.266Å
> label height 2
> ~distance #1/B:149@CA #1/C:149@CA
> ~distance #1/B:151@CA #1/C:151@CA
> ~distance #1/B:153@CA #1/C:153@CA
> ~distance #1/B:155@CA #1/C:155@CA
> ~distance #1/B:157@CA #1/C:157@CA
> ~distance #1/B:159@CA #1/C:159@CA
> ~distance #1/B:161@CA #1/C:161@CA
> ~distance #1/B:163@CA #1/C:163@CA
> ~distance #1/B:165@CA #1/C:165@CA
> ~distance #1/B:167@CA #1/C:167@CA
> ~distance #1/B:169@CA #1/C:169@CA
> select #1/b,c
4909 atoms, 4703 bonds, 5 pseudobonds, 912 residues, 3 models selected
Alignment identifier is 1/B
Alignment identifier is 1/C
> ~select
Nothing selected
> select #1/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #1/C:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> ~select
Nothing selected
> ~distance #1/B:171@CA #1/C:171@CA
> hide #!1 models
> hide #!4 models
> hide #4.1 models
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_C5_chains_renamed.pdb
Chain information for MolBC_WT_in_C5_chains_renamed.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> view
> select add #5
8692 atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.79745,-0.20301,0.56821,-3.4231,-0.56888,-0.56685,0.59586,7.3685,0.20113,-0.79841,-0.56752,20.438
> ui mousemode right zoom
> select #5/B
2354 atoms, 2405 bonds, 2 pseudobonds, 309 residues, 2 models selected
> color (#!5 & sel) blue
> select #5/c
2304 atoms, 2353 bonds, 2 pseudobonds, 303 residues, 2 models selected
> color (#!5 & sel) cornflower blue
> select #5/d
1996 atoms, 2036 bonds, 251 residues, 1 model selected
> color sel purple
> select #5/e
2004 atoms, 2044 bonds, 252 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> select add #5
8692 atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
> select subtract #5
Nothing selected
> select #5/b,c
4658 atoms, 4758 bonds, 4 pseudobonds, 612 residues, 2 models selected
Alignment identifier is 5/B
Alignment identifier is 5/C
> ~select
Nothing selected
> select #5/B:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/B:4-146
942 atoms, 962 bonds, 2 pseudobonds, 125 residues, 2 models selected
> cartoon hide (#!5 & sel)
> select #5/B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/B:172-330
1222 atoms, 1250 bonds, 159 residues, 1 model selected
> cartoon hide sel
> select #5/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:5-146
892 atoms, 910 bonds, 2 pseudobonds, 119 residues, 2 models selected
> cartoon hide (#!5 & sel)
> select #5/C:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:172-330
1222 atoms, 1250 bonds, 159 residues, 1 model selected
> cartoon hide sel
> hide sel atoms
> select #5/d,e
4000 atoms, 4080 bonds, 503 residues, 1 model selected
> cartoon hide sel
> ui mousemode right select
> select clear
Drag select of 34 atoms, 36 bonds
> hide sel atoms
> select add #5
8692 atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #5
8692 atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
> select subtract #5
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> distance #5/B:149@ca #5/C:149@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B MET 149 CA and /C MET
149 CA: 24.861Å
> show #!4 models
> show #4.1 models
> distance #5/B:151@ca #5/C:151@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ILE 151 CA and /C ILE
151 CA: 18.415Å
> distance #5/B:153@ca #5/C:153@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ILE 153 CA and /C ILE
153 CA: 25.604Å
> distance #5/B:155@ca #5/C:155@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B MET 155 CA and /C MET
155 CA: 16.498Å
> distance #5/B:157@ca #5/C:157@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B LEU 157 CA and /C LEU
157 CA: 24.517Å
> distance #5/B:159@ca #5/C:159@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B GLY 159 CA and /C GLY
159 CA: 17.616Å
> distance #5/B:161@ca #5/C:161@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B PHE 161 CA and /C PHE
161 CA: 21.963Å
> distance #5/B:163@ca #5/C:163@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ALA 163 CA and /C ALA
163 CA: 19.560Å
> distance #5/B:165@ca #5/C:165@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B VAL 165 CA and /C VAL
165 CA: 17.433Å
> distance #5/B:167@ca #5/C:167@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B LEU 167 CA and /C LEU
167 CA: 21.738Å
> distance #5/B:169@ca #5/C:169@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B GLN 169 CA and /C GLN
169 CA: 13.848Å
> distance #5/B:171@ca #5/C:171@ca color black
Distance between MolBC_WT_in_C5_chains_renamed.pdb #5/B ILE 171 CA and /C ILE
171 CA: 22.420Å
> label height 2
> label height 1.5
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!4 models
> show #!4 models
> surface #4-5
> transparency #4-5 60
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> label height 3
> label height 2.5
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ~distance #5/B:149@CA #5/C:149@CA
> ~distance #5/B:151@CA #5/C:151@CA
> ~distance #5/B:153@CA #5/C:153@CA
> ~distance #5/B:155@CA #5/C:155@CA
> ~distance #5/B:157@CA #5/C:157@CA
> ~distance #5/B:159@CA #5/C:159@CA
> ~distance #5/B:161@CA #5/C:161@CA
> ~distance #5/B:163@CA #5/C:163@CA
> ~distance #5/B:165@CA #5/C:165@CA
> ~distance #5/B:167@CA #5/C:167@CA
> ~distance #5/B:169@CA #5/C:169@CA
> ~distance #5/B:171@CA #5/C:171@CA
> hide #!5 models
> open
> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc.pdb
Chain information for MolABC_no_nuc.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> view
> select #7/B:6-325
2441 atoms, 2496 bonds, 320 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #7
11335 atoms, 11571 bonds, 1 pseudobond, 1452 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select #7/a
2485 atoms, 2532 bonds, 1 pseudobond, 313 residues, 2 models selected
> color (#!7 & sel) orange
> color (#!7 & sel) yellow
> select #7/b
2441 atoms, 2496 bonds, 320 residues, 1 model selected
> color sel blue
> select #7/c
2411 atoms, 2465 bonds, 316 residues, 1 model selected
> color sel cornflower blue
> select #7/d
2003 atoms, 2043 bonds, 252 residues, 1 model selected
> color sel purple
> select #7/e
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> ui mousemode right zoom
> select add #7
11335 atoms, 11571 bonds, 1 pseudobond, 1452 residues, 2 models selected
> ~select
Nothing selected
> select #7/a,d,e
6483 atoms, 6610 bonds, 1 pseudobond, 816 residues, 2 models selected
> cartoon hide (#!7 & sel)
> select #7/b,c
4852 atoms, 4961 bonds, 636 residues, 1 model selected
Alignment identifier is 7/B
Alignment identifier is 7/C
> ~select
Nothing selected
> select #7/B:62
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/B:62-87
184 atoms, 185 bonds, 26 residues, 1 model selected
> ~select
Nothing selected
> select #7/B:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/B:6-146
1074 atoms, 1099 bonds, 141 residues, 1 model selected
> cartoon hide sel
> select #7/B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/B:172-325
1177 atoms, 1204 bonds, 154 residues, 1 model selected
> cartoon hide sel
> select #7/C:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/C:6-148
1090 atoms, 1115 bonds, 143 residues, 1 model selected
> cartoon hide sel
> select #7/C:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/C:172-321
1147 atoms, 1173 bonds, 150 residues, 1 model selected
> cartoon hide sel
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-0.46625,0,1,0,0.10077,0,0,1,11.839
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,0.78501,0,1,0,-0.25841,0,0,1,8.9345
> distance #7/B:171@ca #7/C:171@ca color black
Distance between MolABC_no_nuc.pdb #7/B ILE 171 CA and /C ILE 171 CA: 23.719Å
> distance #7/B:169@ca #7/C:169@ca color black
Distance between MolABC_no_nuc.pdb #7/B GLN 169 CA and /C GLN 169 CA: 15.265Å
> distance #7/B:167@ca #7/C:167@ca color black
Distance between MolABC_no_nuc.pdb #7/B LEU 167 CA and /C LEU 167 CA: 22.879Å
> distance #7/B:165@ca #7/C:165@ca color black
Distance between MolABC_no_nuc.pdb #7/B VAL 165 CA and /C VAL 165 CA: 18.972Å
> distance #7/B:163@ca #7/C:163@ca color black
Distance between MolABC_no_nuc.pdb #7/B ALA 163 CA and /C ALA 163 CA: 20.705Å
> distance #7/B:161@ca #7/C:161@ca color black
Distance between MolABC_no_nuc.pdb #7/B PHE 161 CA and /C PHE 161 CA: 23.247Å
> distance #7/B:159@ca #7/C:159@ca color black
Distance between MolABC_no_nuc.pdb #7/B GLY 159 CA and /C GLY 159 CA: 18.386Å
> distance #7/B:157@ca #7/C:157@ca color black
Distance between MolABC_no_nuc.pdb #7/B LEU 157 CA and /C LEU 157 CA: 25.664Å
> distance #7/B:155@ca #7/C:155@ca color black
Distance between MolABC_no_nuc.pdb #7/B MET 155 CA and /C MET 155 CA: 17.226Å
> distance #7/B:153@ca #7/C:153@ca color black
Distance between MolABC_no_nuc.pdb #7/B ILE 153 CA and /C ILE 153 CA: 26.547Å
> distance #7/B:151@ca #7/C:151@ca color black
Distance between MolABC_no_nuc.pdb #7/B ILE 151 CA and /C ILE 151 CA: 18.605Å
> distance #7/B:149@ca #7/C:149@ca color black
Distance between MolABC_no_nuc.pdb #7/B MET 149 CA and /C MET 149 CA: 25.434Å
> label height 1.5
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ui mousemode right zoom
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> select add #7
11335 atoms, 11571 bonds, 13 pseudobonds, 1452 residues, 3 models selected
> select subtract #7
Nothing selected
> select #7/B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/B:172-325
1177 atoms, 1204 bonds, 154 residues, 1 model selected
> select #7/B:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/B:27-34
62 atoms, 62 bonds, 8 residues, 1 model selected
> matchmaker #3/b:147-185 to #7/b:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc.pdb, chain B (#7) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 186.6
RMSD between 39 pruned atom pairs is 0.343 angstroms; (across all 39 pairs:
0.343)
> select add #7
11335 atoms, 11571 bonds, 13 pseudobonds, 1452 residues, 3 models selected
> select subtract #7
Nothing selected
> show #!3 models
> surface hidePatches #3-4,7
> color #3 darkgrey
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!7 models
> select #7
11335 atoms, 11571 bonds, 13 pseudobonds, 1452 residues, 3 models selected
> surface (#!7 & sel)
> transparency (#!7 & sel) 60
> select add #4
11335 atoms, 11571 bonds, 15 pseudobonds, 1452 residues, 9 models selected
> select subtract #4
11335 atoms, 11571 bonds, 1 pseudobond, 1452 residues, 7 models selected
> select subtract #7
5 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> label height 2.5
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ~distance #7/B:149@CA #7/C:149@CA
> ~distance #7/B:151@CA #7/C:151@CA
> ~distance #7/B:153@CA #7/C:153@CA
> ~distance #7/B:155@CA #7/C:155@CA
> ~distance #7/B:157@CA #7/C:157@CA
> ~distance #7/B:159@CA #7/C:159@CA
> ~distance #7/B:161@CA #7/C:161@CA
> ~distance #7/B:163@CA #7/C:163@CA
> ~distance #7/B:165@CA #7/C:165@CA
> ~distance #7/B:169@CA #7/C:169@CA
> ~distance #7/B:167@CA #7/C:167@CA
> distance #7/B:169@ca #7/C:169@ca color black
Distance between MolABC_no_nuc.pdb #7/B GLN 169 CA and /C GLN 169 CA: 15.265Å
> label height 2.5
[Repeated 1 time(s)]
> ~distance #7/B:169@CA #7/C:169@CA
> ~distance #7/B:171@CA #7/C:171@CA
> hide #!7 models
> open /Users/alexandrakaragiaridi/Desktop/MolABC_nuc_chains_renamed.pdb
Chain information for MolABC_nuc_chains_renamed.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D E | No description available
> ui mousemode right "translate selected models"
> view
> select #8
10337 atoms, 10549 bonds, 4 pseudobonds, 1316 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #8/A:23-341
1487 atoms, 1510 bonds, 3 pseudobonds, 187 residues, 2 models selected
> color (#!8 & sel) yellow
> select #8/B:7-331
2278 atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
> color (#!8 & sel) blue
> select #8/C:6-331
2494 atoms, 2550 bonds, 326 residues, 1 model selected
> color sel cornflower blue
> select #8/D:2-252
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> color sel purple
> select #8/E:2-252
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> select #8/b,c
4772 atoms, 4877 bonds, 1 pseudobond, 625 residues, 2 models selected
Alignment identifier is 8/B
Alignment identifier is 8/C
> ~select
Nothing selected
> select #8/B:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:7-146
858 atoms, 876 bonds, 1 pseudobond, 114 residues, 2 models selected
> cartoon hide (#!8 & sel)
> select #8/B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:172-331
1230 atoms, 1258 bonds, 160 residues, 1 model selected
> cartoon hide sel
> select #8/C:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/C:6-146
1074 atoms, 1099 bonds, 141 residues, 1 model selected
> cartoon hide sel
> select #8/C:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/C:172-331
1230 atoms, 1258 bonds, 160 residues, 1 model selected
> cartoon hide sel
> ~select
Nothing selected
> select #8/a,d,e
5477 atoms, 5580 bonds, 3 pseudobonds, 689 residues, 2 models selected
> hide sel cartoons
> select add #8
10337 atoms, 10549 bonds, 4 pseudobonds, 1316 residues, 2 models selected
> select subtract #8
Nothing selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> matchmaker #3/b:147-185 to #8/b:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_chains_renamed.pdb, chain B (#8) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 190.2
RMSD between 39 pruned atom pairs is 0.552 angstroms; (across all 39 pairs:
0.552)
> show #!3 models
> hide #!3 models
> distance #7/B:171@ca #7/C:171@ca color black
Distance between MolABC_no_nuc.pdb #7/B ILE 171 CA and /C ILE 171 CA: 23.719Å
> distance #8/B:171@ca #8/C:171@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B ILE 171 CA and /C ILE 171
CA: 23.083Å
> distance #8/B:169@ca #8/C:169@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B GLN 169 CA and /C GLN 169
CA: 15.069Å
> distance #8/B:167@ca #8/C:167@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B LEU 167 CA and /C LEU 167
CA: 22.924Å
> distance #8/B:165@ca #8/C:165@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B VAL 165 CA and /C VAL 165
CA: 19.082Å
> distance #8/B:163@ca #8/C:163@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B ALA 163 CA and /C ALA 163
CA: 21.089Å
> distance #8/B:161@ca #8/C:161@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B PHE 161 CA and /C PHE 161
CA: 24.043Å
> distance #8/B:159@ca #8/C:159@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B GLY 159 CA and /C GLY 159
CA: 19.297Å
> distance #8/B:157@ca #8/C:157@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B LEU 157 CA and /C LEU 157
CA: 26.623Å
> distance #8/B:155@ca #8/C:155@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B MET 155 CA and /C MET 155
CA: 18.196Å
> distance #8/B:153@ca #8/C:153@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B ILE 153 CA and /C ILE 153
CA: 27.497Å
> distance #8/B:151@ca #8/C:151@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B ILE 151 CA and /C ILE 151
CA: 18.896Å
> distance #8/B:149@ca #8/C:149@ca color black
Distance between MolABC_nuc_chains_renamed.pdb #8/B MET 149 CA and /C MET 149
CA: 26.821Å
> label height 1.5
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> select #8
10337 atoms, 10549 bonds, 16 pseudobonds, 1316 residues, 3 models selected
> show sel surfaces
> transparency (#!8 & sel) 60
> select subtract #8
5 models selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select ::name="ANP"
88 atoms, 92 bonds, 2 residues, 1 model selected
> show sel surfaces
> color (#!8 & sel) forest green
> ~select
Nothing selected
> label height 2.5
[Repeated 1 time(s)]
> ui mousemode right "move label"
> ~distance #7/B:171@CA #7/C:171@CA
> ~distance #8/B:149@CA #8/C:149@CA
> ~distance #8/B:151@CA #8/C:151@CA
> ~distance #8/B:153@CA #8/C:153@CA
> ~distance #8/B:155@CA #8/C:155@CA
> ~distance #8/B:157@CA #8/C:157@CA
> ~distance #8/B:159@CA #8/C:159@CA
> ~distance #8/B:161@CA #8/C:161@CA
> ~distance #8/B:163@CA #8/C:163@CA
> ~distance #8/B:165@CA #8/C:165@CA
> ~distance #8/B:167@CA #8/C:167@CA
> ~distance #8/B:169@CA #8/C:169@CA
> ~distance #8/B:171@CA #8/C:171@CA
> save /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
> hide #!4 models
> hide #4.1 models
> select #8
10337 atoms, 10549 bonds, 4 pseudobonds, 1316 residues, 7 models selected
> cartoon (#!8 & sel)
> select #8/a,d,e
5477 atoms, 5580 bonds, 3 pseudobonds, 689 residues, 2 models selected
> cartoon hide (#!8 & sel)
> surface hidePatches (#!8 & sel)
> select ::name="ANP"
88 atoms, 92 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide sel surfaces
> select #8/d,e
3990 atoms, 4070 bonds, 502 residues, 1 model selected
> show sel surfaces
> ~select
Nothing selected
> hide #!8 models
> show #!3 models
> cartoon #3
> ui mousemode right zoom
> select #3/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!3 & sel) blue
> select #3/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!3 & sel) cornflower blue
> select #3/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> color (#!3 & sel) purple
> select #3/e
1977 atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> show #!5 models
> color #5 darkgrey
> matchmaker #3/b:147-185 to #5/b:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolBC_WT_in_C5_chains_renamed.pdb, chain B (#5) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 186.6
RMSD between 39 pruned atom pairs is 0.534 angstroms; (across all 39 pairs:
0.534)
> view
> hide #!3,5 surfaces
> cartoon #3,5
> morph #3,5 frames 60
Computed 61 frame morph #9
> coordset #9 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!9 models
> hide #4.1 models
> show #!3 models
> color #3 darkgrey
> show #!7 models
> view
> hide #!3 models
> view
> hide #!7 surfaces
> cartoon #7
> matchmaker #3/b:147-185 to #7/b:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc.pdb, chain B (#7) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 186.6
RMSD between 39 pruned atom pairs is 0.343 angstroms; (across all 39 pairs:
0.343)
> show #!3 models
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> morph #7,3 frames 60
models have different number of chains, 5 (Morph - MolABC_no_nuc.pdb #/A,Morph
- MolABC_no_nuc.pdb #/B,Morph - MolABC_no_nuc.pdb #/C,Morph -
MolABC_no_nuc.pdb #/D,Morph - MolABC_no_nuc.pdb #/E) and 4
(MolBC_WT_final_structure_chains_renamed.pdb
#3/B,MolBC_WT_final_structure_chains_renamed.pdb
#3/C,MolBC_WT_final_structure_chains_renamed.pdb
#3/D,MolBC_WT_final_structure_chains_renamed.pdb #3/E)
> open
> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc_MolA_deleted.pdb
Chain information for MolABC_no_nuc_MolA_deleted.pdb #10
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!7 models
> matchmaker #3/b:147-185 to #10/b:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 186.6
RMSD between 39 pruned atom pairs is 0.343 angstroms; (across all 39 pairs:
0.343)
> select #10/b
2441 atoms, 2496 bonds, 320 residues, 1 model selected
> color sel blue
> select #10/c
2411 atoms, 2465 bonds, 316 residues, 1 model selected
> color sel cornflower blue
> select #10/d
2003 atoms, 2043 bonds, 252 residues, 1 model selected
> color sel purple
> select #10/e
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> select #3/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> ~select
Nothing selected
> morph #10,3 frames 60
Computed 61 frame morph #11
> coordset #11 1,61
> ui mousemode right "translate selected models"
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!11 models
> open /Users/alexandrakaragiaridi/Desktop/MolABC_nuc_MolA_deleted.pdb
Chain information for MolABC_nuc_MolA_deleted.pdb #12
---
Chain | Description
B | No description available
C | No description available
D E | No description available
> view
> select #12/b
2278 atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
> color (#!12 & sel) blue
> select #12/c
2494 atoms, 2550 bonds, 326 residues, 1 model selected
> color sel cornflower blue
> select #12/d
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> color sel purple
> select #12/e
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> matchmaker #3/b:147-185 to #12/b:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_MolA_deleted.pdb, chain B (#12) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 190.2
RMSD between 39 pruned atom pairs is 0.552 angstroms; (across all 39 pairs:
0.552)
> show #!3 models
> select add #12
8850 atoms, 9039 bonds, 1 pseudobond, 1129 residues, 2 models selected
> select subtract #12
Nothing selected
> hide #!12 models
> show #!8 models
> surface hidePatches #3,8
> cartoon #3,8
> matchmaker #3/b:147-185 to #8/b:147-185
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_chains_renamed.pdb, chain B (#8) with
MolBC_WT_final_structure_chains_renamed.pdb, chain B (#3), sequence alignment
score = 190.2
RMSD between 39 pruned atom pairs is 0.552 angstroms; (across all 39 pairs:
0.552)
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!8 models
> show #!12 models
> ui mousemode right "translate selected models"
> hide #!12 models
> show #!8 models
> hide #!8 models
> show #!12 models
> morph #12,3 frames 60
Computed 61 frame morph #13
> coordset #13 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> save /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
——— End of log from Fri Apr 4 15:35:46 2025 ———
opened ChimeraX session
> close #13
> close #11
> rename #3 MolBC_WT_final_structure_chains_renamed_cryo.pdb
> show #!3 models
> hide #!3 models
> rename #1 MolBC_in_DM_chains_renamed.pdb
> rename #3 MolBC_WT_in_DDM_chains_renamed_cryo.pdb
> rename #8 MolABC_nuc.pdb
> show #!8 models
> hide #!8 models
> show #!7 models
> ui mousemode right "translate selected models"
> select #7/b
2441 atoms, 2496 bonds, 320 residues, 1 model selected
Alignment identifier is 7/B
> ~select
Nothing selected
> show #!3 models
> select #3/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
Alignment identifier is 3/B
> ~select
Nothing selected
> select #3/B:54-55
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/B:54-86
242 atoms, 243 bonds, 33 residues, 1 model selected
> select #7/B:52
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/B:52-87
267 atoms, 270 bonds, 36 residues, 1 model selected
> matchmaker #3/b:52-87 to #7/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc.pdb, chain B (#7) with
MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
score = 176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> select add #7
11335 atoms, 11571 bonds, 1 pseudobond, 1452 residues, 3 models selected
> select subtract #7
5 models selected
> color #3 #929292ff
> color #3 #919191ff
> color #3 #797979ff
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!7 models
> show #10 models
> matchmaker #3/b:52-87 to #10/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
score = 176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> morph #3,10 frames 60
Computed 61 frame morph #11
> coordset #11 1,61
> hide #!11 models
> show #!3 models
> show #10 models
> morph #10,3 frames 60
Computed 61 frame morph #13
> coordset #13 1,61
> morph #10,3 frames 100
Computed 101 frame morph #14
> coordset #14 1,101
> hide #!13 models
> show #!13 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> close #13
> close #14
> show #!3 models
> show #10 models
> morph #3,10 frames 100
Computed 101 frame morph #13
> coordset #13 1,101
> close #13
> show #!3 models
> show #10 models
> morph #10,3 frames 60
Computed 61 frame morph #13
> coordset #13 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!13 models
> show #!3 models
> show #10 models
> morph #3,10 frames 60
Computed 61 frame morph #14
> coordset #14 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!14 models
> show #!3 models
> show #!8 models
> select #8/b
2278 atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
Alignment identifier is 8/B
> ~select
Nothing selected
> matchmaker #3/b:56-87 to #8/b:56-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc.pdb, chain B (#8) with
MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
score = 161.8
RMSD between 32 pruned atom pairs is 0.522 angstroms; (across all 32 pairs:
0.522)
> view
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #!8 models
> show #!12 models
> matchmaker #3/b:56-87 to #8/b:56-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc.pdb, chain B (#8) with
MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
score = 161.8
RMSD between 32 pruned atom pairs is 0.522 angstroms; (across all 32 pairs:
0.522)
> morph #12,3 frames 60
Computed 61 frame morph #15
> coordset #15 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!15 models
> show #!3 models
> show #!12 models
> morph #3,12 frames 60
Computed 61 frame morph #16
> coordset #16 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!16 models
> show #!3 models
> show #10 models
> matchmaker #3/b:52-87 to #10/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
score = 176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select #3/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!3 & sel) orange
> color (#!3 & sel) orange red
> select #3/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!3 & sel) forest green
> ~select
Nothing selected
> select #3/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> ui tool show "Color Actions"
> color sel saddle brown
> select #3/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> ~select
Nothing selected
> select #3/d,e
3862 atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select #10/d,e
3998 atoms, 4078 bonds, 503 residues, 1 model selected
> cartoon hide sel
> select add #10
8850 atoms, 9039 bonds, 1139 residues, 1 model selected
> select subtract #10
Nothing selected
> ui mousemode right zoom
> ui tool show "Side View"
> ui tool show Axes/Planes/Centroids
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> ui tool show Axes/Planes/Centroids
value: array([ 0, 0, 0, 255], dtype=uint8) default: None
> define axis #3 perHelix true color black name "helix axes"
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 1'
centered at [138.87288781 117.78180224 148.42755497] with direction [
0.0440841 -0.00343284 0.99902193], radius 1.84197, and length 21.5191
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 2'
centered at [136.89511948 119.27405922 134.67479006] with direction [
0.08451804 -0.11156966 0.990156 ], radius 1.44753, and length 7.55249
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 3'
centered at [144.01128977 114.05989748 123.60591038] with direction [0.9545536
0.24888157 0.16396765], radius 1.16133, and length 5.69625
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 4'
centered at [146.98443498 118.23838681 127.30097697] with direction
[0.67184113 0.719126 0.17744662], radius 1.92464, and length 5.88277
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 5'
centered at [150.46413505 128.9089645 146.65778978] with direction [0.21556326
0.47619176 0.85251034], radius 1.85607, and length 39.0284
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 6'
centered at [162.52256844 142.63940295 136.02828041] with direction [
0.27282382 0.02254532 -0.96179981], radius 1.84926, and length 23.1877
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 7'
centered at [168.38900361 139.87104636 144.90354783] with direction
[0.21440203 0.43472652 0.87466829], radius 1.95697, and length 38.1453
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 8'
centered at [161.37459523 151.28871478 143.12819413] with direction
[-0.02791598 0.14852199 -0.98851501], radius 1.84012, and length 35.7778
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 9'
centered at [154.88027968 145.06608012 126.7136637 ] with direction
[-0.53965869 -0.36466803 0.75880546], radius 1.73624, and length 11.5571
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 10'
centered at [152.01490142 141.38744199 133.65031613] with direction
[-0.73611941 -0.00082326 0.67685119], radius 1.13652, and length 5.92586
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 11'
centered at [159.02791703 123.43494192 138.60155144] with direction
[0.21299364 0.08258235 0.97355732], radius 1.85904, and length 16.6781
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 12'
centered at [158.72486474 123.11321475 157.3782829 ] with direction
[-0.3437473 0.03748733 0.93831364], radius 1.80163, and length 7.70168
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 13'
centered at [156.82043946 130.61392236 167.52160805] with direction
[-0.13681146 -0.9079335 -0.39615575], radius 1.76316, and length 8.14729
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 14'
centered at [161.73668965 138.4798262 174.91852687] with direction [
0.08864439 0.92407725 -0.3717841 ], radius 1.56342, and length 5.87844
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 15'
centered at [163.97384547 134.12606164 177.32571777] with direction [
0.28048337 0.89218889 -0.35401705], radius 1.19567, and length 5.28539
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 16'
centered at [161.6792009 133.69839711 150.6143826 ] with direction
[-0.35567372 -0.03245447 -0.93404652], radius 1.90371, and length 32.7461
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 17'
centered at [142.47807596 133.57148003 155.82946554] with direction
[-0.76939881 -0.0574665 0.63617849], radius 1.58457, and length 5.65891
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 18'
centered at [140.21990568 130.59778964 159.96782242] with direction
[-0.66910528 0.00110959 0.7431668 ], radius 1.16549, and length 5.71771
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 19'
centered at [143.31329819 127.50429047 147.60887881] with direction
[-0.34152171 0.19224759 -0.92000206], radius 1.94095, and length 36.4169
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 20'
centered at [139.04079142 140.67324534 145.03288008] with direction
[-0.45861454 0.15994128 0.87412327], radius 1.91368, and length 23.535
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 1'
centered at [163.2294379 183.2483208 147.72816911] with direction [ 0.16232497
-0.06729814 -0.98443972], radius 1.84785, and length 19.9747
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 2'
centered at [166.38264193 181.34888562 135.02965093] with direction [
0.18614011 -0.1161945 -0.97562836], radius 1.46901, and length 7.42552
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 3'
centered at [151.14751531 171.39665553 147.30930401] with direction
[-0.28843731 -0.47151966 0.83335054], radius 1.88144, and length 38.8998
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 4'
centered at [140.48527463 158.01748359 134.72758194] with direction
[-0.19079639 -0.05488875 -0.98009385], radius 1.84209, and length 23.4331
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 5'
centered at [134.27304968 161.20652608 142.78627861] with direction
[-0.24658266 -0.42045288 0.87316457], radius 1.88261, and length 33.9177
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 6'
centered at [140.98274908 150.00170498 143.83752847] with direction [
0.09536412 -0.19142402 -0.97686362], radius 1.85161, and length 39.0487
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 7'
centered at [148.55019275 154.95279448 125.67151223] with direction
[0.33479868 0.28666457 0.89762646], radius 1.71026, and length 10.2146
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 8'
centered at [150.6232085 158.76590252 131.58822087] with direction
[-0.26684054 0.15585634 0.95105464], radius 1.16158, and length 5.76255
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 9'
centered at [143.13144099 177.5436752 142.77452959] with direction
[-0.16046819 0.01701625 0.98689432], radius 1.9463, and length 26.8796
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 10'
centered at [143.02837214 178.22286017 158.7754407 ] with direction
[-0.38096048 -0.31575783 0.86900294], radius 1.20412, and length 5.28596
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 11'
centered at [143.59843255 170.15589851 166.53285951] with direction [
0.04918429 -0.95745313 0.28436667], radius 1.5971, and length 11.0317
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 12'
centered at [137.99810081 163.55370792 173.5505006 ] with direction
[-0.06121785 -0.94362406 -0.32530908], radius 1.57972, and length 5.69983
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 13'
centered at [135.58382444 167.90992901 175.61219975] with direction
[-0.25305438 -0.90434208 -0.34369883], radius 1.19961, and length 5.28161
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 14'
centered at [140.04917237 167.45543663 149.47364086] with direction [
0.41500885 0.01046323 -0.90975721], radius 1.89122, and length 32.139
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 15'
centered at [159.99254977 169.7174672 158.21270651] with direction [0.45613914
0.56166159 0.69027048], radius 1.79128, and length 12.5526
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 16'
centered at [152.43981866 175.99254125 160.74627567] with direction
[-0.29572772 0.05698523 0.95357108], radius 1.81357, and length 7.71215
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 17'
centered at [160.47513667 173.0101247 144.08830691] with direction [
0.43750857 -0.28211725 -0.85381269], radius 1.85399, and length 31.2751
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 18'
centered at [163.57342427 160.32346648 147.29998901] with direction [
0.31244959 -0.09350065 0.94532158], radius 2.0372, and length 26.3918
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 1'
centered at [167.87615649 143.04389693 185.98121469] with direction [ 0.438123
-0.83562973 -0.33131737], radius 1.81012, and length 14.1925
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 2'
centered at [147.6201987 127.68936813 176.62184077] with direction [
0.93725005 0.16662752 -0.30626395], radius 1.56131, and length 6.06092
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 3'
centered at [154.95568202 126.20793828 177.58107552] with direction [
0.95898997 -0.26644434 -0.09667287], radius 1.44573, and length 10.0638
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 4'
centered at [151.15600715 118.6019877 181.57814446] with direction
[-0.37732147 0.56479719 0.73391596], radius 1.79916, and length 17.2473
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 5'
centered at [146.55331579 123.39381244 190.23537683] with direction [
0.04673215 -0.81899731 -0.57189118], radius 1.1843, and length 5.42106
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 6'
centered at [140.73208295 135.93343584 177.58493265] with direction
[-0.81812109 0.45557423 0.35089885], radius 1.15152, and length 5.77568
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 7'
centered at [148.98351106 133.34372209 185.7268084 ] with direction [
0.77026349 -0.62284617 -0.13695546], radius 1.81761, and length 18.4936
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 8'
centered at [157.23115414 125.30149438 184.62927987] with direction [
0.67554073 -0.41725825 -0.60789825], radius 1.1514, and length 5.8277
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 9'
centered at [150.063202 134.06961112 197.9082053 ] with direction [ 0.72695201
-0.66523867 0.17028885], radius 1.85312, and length 24.2887
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 10'
centered at [155.63590787 142.9646218 203.72317399] with direction
[-0.12131521 0.97595014 -0.1811186 ], radius 1.6972, and length 11.4219
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 11'
centered at [165.59051581 144.79740981 209.25865921] with direction [
4.40157598e-01 8.97920524e-01 -1.47057412e-04], radius 1.57329, and length
5.79026
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 12'
centered at [163.52091577 156.28680447 205.36494461] with direction [
0.06439306 -0.36066782 0.93046884], radius 1.86281, and length 11.8846
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 1'
centered at [130.87501269 159.11892998 184.2442496 ] with direction
[-0.40949696 0.82601253 -0.3873184 ], radius 1.80496, and length 14.0558
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 2'
centered at [151.85163649 174.25343037 176.03807778] with direction
[-0.92231263 -0.17427807 -0.34491532], radius 1.56122, and length 5.9922
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 3'
centered at [144.50157861 175.78058157 176.35465875] with direction
[-0.94732324 0.25522088 -0.19349673], radius 1.44096, and length 10.1801
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 4'
centered at [148.57410773 182.91758455 181.91135025] with direction [
0.33102847 -0.46584117 0.82061694], radius 1.85479, and length 20.4498
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 5'
centered at [159.11810243 177.16289377 183.66867963] with direction [
0.28986355 -0.6503084 -0.70219521], radius 1.14027, and length 5.99708
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 6'
centered at [149.76839231 168.9091345 185.16992042] with direction
[-0.75513013 0.61647857 -0.22300821], radius 1.81515, and length 18.5125
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 7'
centered at [141.64126568 176.89330933 183.09126614] with direction
[-0.62885264 0.41150727 -0.65970155], radius 1.14434, and length 5.9151
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 8'
centered at [147.24134326 169.09583718 197.32862548] with direction
[-0.71026615 0.69813961 0.09012817], radius 1.90461, and length 25.5463
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 9'
centered at [141.63445911 159.08325547 202.95746234] with direction
[-0.06815874 0.94742795 0.31262545], radius 1.63707, and length 10.4006
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 10'
centered at [131.09207528 158.14926242 207.79433463] with direction
[-0.49510089 -0.86657585 -0.06262105], radius 1.57904, and length 5.37778
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 11'
centered at [133.55097158 146.50628731 204.2284949 ] with direction
[-0.15420662 0.41363509 0.89728832], radius 1.8638, and length 11.9168
chain B helix 1 #3.6.1 to chain B helix 2 #3.6.2: distance: 1.279Å; angle:
6.6°
> select down
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> select down
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> select down
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> select down
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> select down
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> close #3.6.1-61
> ui tool show Axes/Planes/Centroids
value: array([ 0, 0, 0, 255], dtype=uint8) default: None
> define axis #3 perHelix true color black name "helix axes" radius 0.2
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 1'
centered at [138.87288781 117.78180224 148.42755497] with direction [
0.0440841 -0.00343284 0.99902193], radius 0.2, and length 21.5191
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 2'
centered at [136.89511948 119.27405922 134.67479006] with direction [
0.08451804 -0.11156966 0.990156 ], radius 0.2, and length 7.55249
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 3'
centered at [144.01128977 114.05989748 123.60591038] with direction [0.9545536
0.24888157 0.16396765], radius 0.2, and length 5.69625
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 4'
centered at [146.98443498 118.23838681 127.30097697] with direction
[0.67184113 0.719126 0.17744662], radius 0.2, and length 5.88277
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 5'
centered at [150.46413505 128.9089645 146.65778978] with direction [0.21556326
0.47619176 0.85251034], radius 0.2, and length 39.0284
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 6'
centered at [162.52256844 142.63940295 136.02828041] with direction [
0.27282382 0.02254532 -0.96179981], radius 0.2, and length 23.1877
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 7'
centered at [168.38900361 139.87104636 144.90354783] with direction
[0.21440203 0.43472652 0.87466829], radius 0.2, and length 38.1453
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 8'
centered at [161.37459523 151.28871478 143.12819413] with direction
[-0.02791598 0.14852199 -0.98851501], radius 0.2, and length 35.7778
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 9'
centered at [154.88027968 145.06608012 126.7136637 ] with direction
[-0.53965869 -0.36466803 0.75880546], radius 0.2, and length 11.5571
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 10'
centered at [152.01490142 141.38744199 133.65031613] with direction
[-0.73611941 -0.00082326 0.67685119], radius 0.2, and length 5.92586
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 11'
centered at [159.02791703 123.43494192 138.60155144] with direction
[0.21299364 0.08258235 0.97355732], radius 0.2, and length 16.6781
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 12'
centered at [158.72486474 123.11321475 157.3782829 ] with direction
[-0.3437473 0.03748733 0.93831364], radius 0.2, and length 7.70168
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 13'
centered at [156.82043946 130.61392236 167.52160805] with direction
[-0.13681146 -0.9079335 -0.39615575], radius 0.2, and length 8.14729
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 14'
centered at [161.73668965 138.4798262 174.91852687] with direction [
0.08864439 0.92407725 -0.3717841 ], radius 0.2, and length 5.87844
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 15'
centered at [163.97384547 134.12606164 177.32571777] with direction [
0.28048337 0.89218889 -0.35401705], radius 0.2, and length 5.28539
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 16'
centered at [161.6792009 133.69839711 150.6143826 ] with direction
[-0.35567372 -0.03245447 -0.93404652], radius 0.2, and length 32.7461
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 17'
centered at [142.47807596 133.57148003 155.82946554] with direction
[-0.76939881 -0.0574665 0.63617849], radius 0.2, and length 5.65891
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 18'
centered at [140.21990568 130.59778964 159.96782242] with direction
[-0.66910528 0.00110959 0.7431668 ], radius 0.2, and length 5.71771
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 19'
centered at [143.31329819 127.50429047 147.60887881] with direction
[-0.34152171 0.19224759 -0.92000206], radius 0.2, and length 36.4169
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain B helix 20'
centered at [139.04079142 140.67324534 145.03288008] with direction
[-0.45861454 0.15994128 0.87412327], radius 0.2, and length 23.535
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 1'
centered at [163.2294379 183.2483208 147.72816911] with direction [ 0.16232497
-0.06729814 -0.98443972], radius 0.2, and length 19.9747
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 2'
centered at [166.38264193 181.34888562 135.02965093] with direction [
0.18614011 -0.1161945 -0.97562836], radius 0.2, and length 7.42552
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 3'
centered at [151.14751531 171.39665553 147.30930401] with direction
[-0.28843731 -0.47151966 0.83335054], radius 0.2, and length 38.8998
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 4'
centered at [140.48527463 158.01748359 134.72758194] with direction
[-0.19079639 -0.05488875 -0.98009385], radius 0.2, and length 23.4331
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 5'
centered at [134.27304968 161.20652608 142.78627861] with direction
[-0.24658266 -0.42045288 0.87316457], radius 0.2, and length 33.9177
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 6'
centered at [140.98274908 150.00170498 143.83752847] with direction [
0.09536412 -0.19142402 -0.97686362], radius 0.2, and length 39.0487
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 7'
centered at [148.55019275 154.95279448 125.67151223] with direction
[0.33479868 0.28666457 0.89762646], radius 0.2, and length 10.2146
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 8'
centered at [150.6232085 158.76590252 131.58822087] with direction
[-0.26684054 0.15585634 0.95105464], radius 0.2, and length 5.76255
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 9'
centered at [143.13144099 177.5436752 142.77452959] with direction
[-0.16046819 0.01701625 0.98689432], radius 0.2, and length 26.8796
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 10'
centered at [143.02837214 178.22286017 158.7754407 ] with direction
[-0.38096048 -0.31575783 0.86900294], radius 0.2, and length 5.28596
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 11'
centered at [143.59843255 170.15589851 166.53285951] with direction [
0.04918429 -0.95745313 0.28436667], radius 0.2, and length 11.0317
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 12'
centered at [137.99810081 163.55370792 173.5505006 ] with direction
[-0.06121785 -0.94362406 -0.32530908], radius 0.2, and length 5.69983
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 13'
centered at [135.58382444 167.90992901 175.61219975] with direction
[-0.25305438 -0.90434208 -0.34369883], radius 0.2, and length 5.28161
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 14'
centered at [140.04917237 167.45543663 149.47364086] with direction [
0.41500885 0.01046323 -0.90975721], radius 0.2, and length 32.139
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 15'
centered at [159.99254977 169.7174672 158.21270651] with direction [0.45613914
0.56166159 0.69027048], radius 0.2, and length 12.5526
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 16'
centered at [152.43981866 175.99254125 160.74627567] with direction
[-0.29572772 0.05698523 0.95357108], radius 0.2, and length 7.71215
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 17'
centered at [160.47513667 173.0101247 144.08830691] with direction [
0.43750857 -0.28211725 -0.85381269], radius 0.2, and length 31.2751
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain C helix 18'
centered at [163.57342427 160.32346648 147.29998901] with direction [
0.31244959 -0.09350065 0.94532158], radius 0.2, and length 26.3918
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 1'
centered at [167.87615649 143.04389693 185.98121469] with direction [ 0.438123
-0.83562973 -0.33131737], radius 0.2, and length 14.1925
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 2'
centered at [147.6201987 127.68936813 176.62184077] with direction [
0.93725005 0.16662752 -0.30626395], radius 0.2, and length 6.06092
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 3'
centered at [154.95568202 126.20793828 177.58107552] with direction [
0.95898997 -0.26644434 -0.09667287], radius 0.2, and length 10.0638
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 4'
centered at [151.15600715 118.6019877 181.57814446] with direction
[-0.37732147 0.56479719 0.73391596], radius 0.2, and length 17.2473
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 5'
centered at [146.55331579 123.39381244 190.23537683] with direction [
0.04673215 -0.81899731 -0.57189118], radius 0.2, and length 5.42106
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 6'
centered at [140.73208295 135.93343584 177.58493265] with direction
[-0.81812109 0.45557423 0.35089885], radius 0.2, and length 5.77568
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 7'
centered at [148.98351106 133.34372209 185.7268084 ] with direction [
0.77026349 -0.62284617 -0.13695546], radius 0.2, and length 18.4936
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 8'
centered at [157.23115414 125.30149438 184.62927987] with direction [
0.67554073 -0.41725825 -0.60789825], radius 0.2, and length 5.8277
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 9'
centered at [150.063202 134.06961112 197.9082053 ] with direction [ 0.72695201
-0.66523867 0.17028885], radius 0.2, and length 24.2887
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 10'
centered at [155.63590787 142.9646218 203.72317399] with direction
[-0.12131521 0.97595014 -0.1811186 ], radius 0.2, and length 11.4219
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 11'
centered at [165.59051581 144.79740981 209.25865921] with direction [
4.40157598e-01 8.97920524e-01 -1.47057412e-04], radius 0.2, and length 5.79026
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain D helix 12'
centered at [163.52091577 156.28680447 205.36494461] with direction [
0.06439306 -0.36066782 0.93046884], radius 0.2, and length 11.8846
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 1'
centered at [130.87501269 159.11892998 184.2442496 ] with direction
[-0.40949696 0.82601253 -0.3873184 ], radius 0.2, and length 14.0558
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 2'
centered at [151.85163649 174.25343037 176.03807778] with direction
[-0.92231263 -0.17427807 -0.34491532], radius 0.2, and length 5.9922
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 3'
centered at [144.50157861 175.78058157 176.35465875] with direction
[-0.94732324 0.25522088 -0.19349673], radius 0.2, and length 10.1801
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 4'
centered at [148.57410773 182.91758455 181.91135025] with direction [
0.33102847 -0.46584117 0.82061694], radius 0.2, and length 20.4498
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 5'
centered at [159.11810243 177.16289377 183.66867963] with direction [
0.28986355 -0.6503084 -0.70219521], radius 0.2, and length 5.99708
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 6'
centered at [149.76839231 168.9091345 185.16992042] with direction
[-0.75513013 0.61647857 -0.22300821], radius 0.2, and length 18.5125
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 7'
centered at [141.64126568 176.89330933 183.09126614] with direction
[-0.62885264 0.41150727 -0.65970155], radius 0.2, and length 5.9151
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 8'
centered at [147.24134326 169.09583718 197.32862548] with direction
[-0.71026615 0.69813961 0.09012817], radius 0.2, and length 25.5463
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 9'
centered at [141.63445911 159.08325547 202.95746234] with direction
[-0.06815874 0.94742795 0.31262545], radius 0.2, and length 10.4006
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 10'
centered at [131.09207528 158.14926242 207.79433463] with direction
[-0.49510089 -0.86657585 -0.06262105], radius 0.2, and length 5.37778
Axis 'MolBC_WT_in_DDM_chains_renamed_cryo.pdb #3/helix axes/chain E helix 11'
centered at [133.55097158 146.50628731 204.2284949 ] with direction
[-0.15420662 0.41363509 0.89728832], radius 0.2, and length 11.9168
value: array([255, 212, 121, 255], dtype=uint8) default: None
> define axis #10 perHelix true color #ffd479 name "helix axes" radius 0.2
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 1' centered
at [138.89432873 118.0602333 148.78947106] with direction [-0.03321708
-0.02481161 -0.99914014], radius 0.2, and length 21.8343
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 2' centered
at [137.22470514 119.20230369 134.81783977] with direction [-0.01245078
0.08491942 -0.99631003], radius 0.2, and length 7.63264
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 3' centered
at [138.05372817 108.06764281 128.51475989] with direction [ 0.8026101
-0.59184527 0.07440569], radius 0.2, and length 18.5767
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 4' centered
at [145.72161104 116.33145977 124.84189419] with direction [0.1508822
0.53938742 0.8284297 ], radius 0.2, and length 16.9619
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 5' centered
at [150.81669695 129.65128059 147.93503227] with direction [0.22863824
0.50193185 0.83413966], radius 0.2, and length 38.3494
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 6' centered
at [155.28565702 143.07274943 150.93031609] with direction [0.52188408
0.82517202 0.21616696], radius 0.2, and length 6.46639
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 7' centered
at [161.4682541 142.4935721 136.67182626] with direction [ 0.20901679
-0.00098958 -0.97791155], radius 0.2, and length 21.903
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 8' centered
at [167.8756954 139.366525 144.05325253] with direction [0.21956307 0.43124242
0.87511258], radius 0.2, and length 36.8449
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 9' centered
at [160.91926351 150.94322402 144.77402766] with direction [-0.05428096
0.15150463 -0.98696501], radius 0.2, and length 38.4235
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 10' centered
at [153.16255893 144.72955059 127.98594293] with direction [-0.39611073
-0.47095447 0.7882247 ], radius 0.2, and length 12.3565
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 11' centered
at [159.05351081 123.17544409 145.89835395] with direction [0.04832853
0.00678212 0.99880847], radius 0.2, and length 30.5075
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 12' centered
at [156.62467727 129.23983617 166.64295286] with direction [-0.60476875
0.72433613 0.33104672], radius 0.2, and length 5.7345
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 13' centered
at [157.41472133 133.74646525 168.35308858] with direction [ 0.28281302
-0.91915742 0.27416498], radius 0.2, and length 5.7588
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 14' centered
at [163.09860358 136.86333389 175.22680129] with direction [ 0.34520149
-0.79444064 0.49969992], radius 0.2, and length 10.8468
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 15' centered
at [161.69075667 133.55055861 150.55871106] with direction [-0.36743289
-0.02621678 -0.92968046], radius 0.2, and length 32.6292
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 16' centered
at [141.58698056 132.34284382 157.58710316] with direction [-0.29675497
-0.608367 0.73608836], radius 0.2, and length 15.2808
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 17' centered
at [143.12102326 127.70175984 146.94348142] with direction [-0.3506446
0.18488988 -0.9180763 ], radius 0.2, and length 37.8351
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain B helix 18' centered
at [138.4415738 140.61248037 144.71229819] with direction [-0.44904978
0.15017058 0.88079685], radius 0.2, and length 22.7906
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 1' centered
at [163.29064596 182.64512887 148.75598259] with direction [-0.05834301
0.00278421 0.99829271], radius 0.2, and length 21.7356
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 2' centered
at [165.21133484 181.2794909 134.90715963] with direction [-0.06092366
0.07495203 0.99532432], radius 0.2, and length 7.38453
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 3' centered
at [164.53561146 192.4729011 128.65578467] with direction [-0.81244329
0.5813858 0.04389144], radius 0.2, and length 18.5121
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 4' centered
at [157.45680002 184.37817105 123.8528681 ] with direction [-0.32193823
-0.50009725 0.80390206], radius 0.2, and length 14.3044
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 5' centered
at [151.36637968 172.18926675 146.45943825] with direction [-0.2624205
-0.46650916 0.84469206], radius 0.2, and length 38.9625
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 6' centered
at [139.79168852 158.62661407 136.63319875] with direction [-0.20785876
-0.01337435 -0.97806741], radius 0.2, and length 21.8971
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 7' centered
at [133.6554324 161.4499327 144.85609143] with direction [-0.24901695
-0.43824913 0.86367139], radius 0.2, and length 28.8519
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 8' centered
at [140.13677409 149.89764288 143.42844734] with direction [ 0.05595601
-0.15755276 -0.98592396], radius 0.2, and length 35.6621
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 9' centered
at [148.28963686 155.95675428 127.59072569] with direction [0.45002321
0.52608488 0.72160503], radius 0.2, and length 9.98349
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 10' centered
at [150.0577348 159.38419006 133.64248285] with direction [ 0.65314182
-0.01925877 0.75699066], radius 0.2, and length 5.7923
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 11' centered
at [142.89437046 178.30495372 145.65238848] with direction [-0.06655957
-0.00993754 0.99773296], radius 0.2, and length 30.3111
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 12' centered
at [144.66131052 173.82859124 165.72848631] with direction [-0.12653854
-0.9912196 -0.03836286], radius 0.2, and length 5.90297
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 13' centered
at [143.98287464 167.83074192 168.24932632] with direction [-0.27621718
0.93078782 0.23945377], radius 0.2, and length 5.71805
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 14' centered
at [138.04156465 165.70742773 175.38542078] with direction [-0.22092881
0.89691282 0.38306377], radius 0.2, and length 11.423
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 15' centered
at [139.6405478 167.88023035 151.11277642] with direction [ 0.3546893
0.01839823 -0.93480319], radius 0.2, and length 34.6455
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 16' centered
at [160.210276 168.69872157 158.12497637] with direction [0.49255082
0.48463911 0.7228545 ], radius 0.2, and length 12.405
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 17' centered
at [158.65506626 173.21794452 146.9061338 ] with direction [ 0.34973132
-0.20483791 -0.91418239], radius 0.2, and length 37.8498
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain C helix 18' centered
at [161.04181351 161.02595429 140.82768715] with direction [ 0.62687875
-0.11819244 0.77009972], radius 0.2, and length 14.1207
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 1' centered
at [168.76700144 141.7958998 185.53240035] with direction [ 0.41814452
-0.85006236 -0.32023295], radius 0.2, and length 14.3046
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 2' centered
at [148.24594739 127.49258116 176.58352434] with direction [ 0.94351814
0.14475109 -0.29802793], radius 0.2, and length 5.90175
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 3' centered
at [155.45300825 125.8189693 177.34230037] with direction [ 0.94930299
-0.28394858 -0.13489639], radius 0.2, and length 10.0409
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 4' centered
at [151.10493761 119.20162945 182.35952123] with direction [-0.37011828
0.49951086 0.78326328], radius 0.2, and length 14.4107
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 5' centered
at [147.40439667 123.05661258 190.19266188] with direction [-0.00875559
-0.79589813 -0.60536725], radius 0.2, and length 5.44482
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 6' centered
at [141.57140032 136.12936891 177.8823915 ] with direction [-0.77937561
0.4911306 0.38905578], radius 0.2, and length 5.93556
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 7' centered
at [149.95074934 133.06815503 185.7198464 ] with direction [ 0.74252233
-0.64996276 -0.16189194], radius 0.2, and length 18.616
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 8' centered
at [157.89141083 124.64099433 184.3669659 ] with direction [ 0.63240665
-0.47596771 -0.61116002], radius 0.2, and length 6.00605
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 9' centered
at [151.32947596 133.32780545 197.91343184] with direction [ 0.71144945
-0.68998224 0.13328237], radius 0.2, and length 24.2622
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 10' centered
at [157.32927478 142.29031805 203.75612885] with direction [ 0.08528956
-0.98386135 0.15729762], radius 0.2, and length 11.4332
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 11' centered
at [167.45280133 143.21626877 209.07861051] with direction [ 0.51964799
0.85435156 -0.00702718], radius 0.2, and length 5.78006
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain D helix 12' centered
at [165.55567951 155.12922861 205.26760417] with direction [ 0.14497464
-0.39113787 0.90884186], radius 0.2, and length 12.0269
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 1' centered
at [133.39473484 157.07146631 185.87999495] with direction [-0.39860215
0.88157301 -0.2528742 ], radius 0.2, and length 19.4134
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 2' centered
at [153.07830876 173.80337272 176.46874051] with direction [-0.94017596
-0.14546857 -0.30807153], radius 0.2, and length 6.02798
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 3' centered
at [146.70080408 175.02852424 177.22092458] with direction [-9.91926295e-01
3.33135128e-04 -1.26815273e-01], radius 0.2, and length 7.52775
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 4' centered
at [150.481171 182.85501584 182.3381486 ] with direction [ 0.32582667
-0.48308072 0.81269306], radius 0.2, and length 20.9936
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 5' centered
at [160.68109744 176.30491972 183.96304867] with direction [ 0.24314391
-0.60924617 -0.75478484], radius 0.2, and length 6.12268
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 6' centered
at [159.7829355 165.1504365 177.91728631] with direction [ 0.80732077
-0.4232423 0.41121665], radius 0.2, and length 5.72695
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 7' centered
at [151.26069892 168.44683323 185.62348711] with direction [-0.73463437
0.65423124 -0.17970486], radius 0.2, and length 18.5879
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 8' centered
at [143.49635171 176.86572021 184.07650532] with direction [-0.61488979
0.45748837 -0.6423511 ], radius 0.2, and length 5.84625
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 9' centered
at [149.7592522 168.1814334 197.81316584] with direction [-0.71101184
0.69313967 0.11840424], radius 0.2, and length 24.3445
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 10' centered
at [143.7666456 159.45212789 203.61703639] with direction [ 0.08102842
-0.98798961 -0.13157097], radius 0.2, and length 11.5155
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 11' centered
at [133.80269407 159.30297004 209.29743794] with direction [-0.52713162
-0.58705225 0.61441184], radius 0.2, and length 5.77119
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/helix axes/chain E helix 12' centered
at [135.3884304 146.52843308 205.04864675] with direction [-0.12217055
0.41913337 0.89966748], radius 0.2, and length 11.9003
chain D helix 1 #3.7.39 to chain D helix 2 #3.7.40: distance: 15.139Å; angle:
68.1°
> close #3.7.39-61
chain E helix 10 to chain E helix 11: distance: 6.298Å; angle: 70.2°
chain E helix 11 #10.1.59 to chain E helix 12 #10.1.60: distance: 7.725Å;
angle: 68.2°
> close #10.1.37-60
chain E helix 11 to chain E helix 12: distance: 7.725Å; angle: 68.2°
> ui mousemode right "translate selected models"
> select #3.7.1
1 model selected
> select #10/d,e
3998 atoms, 4078 bonds, 503 residues, 1 model selected
> cartoon sel
> select #3/d,e
3862 atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
> cartoon (#!3 & sel)
> view matrix models
> #3,0.96671,0.25077,0.050765,-11.242,0.25302,-0.96646,-0.043981,247.19,0.038033,0.055362,-0.99774,263.7,#4,1,0,0,0,0,1,0,0,0,0,1,0
> matchmaker #3/b:52-87 to #10/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
score = 176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> select #3.7.1
1 model selected
> ~select #3.7.1
Nothing selected
> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
> select #10/d,e
3998 atoms, 4078 bonds, 503 residues, 1 model selected
> cartoon hide sel
> select #3/d,e
3862 atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select add #4
3862 atoms, 3935 bonds, 6 pseudobonds, 486 residues, 6 models selected
> select subtract #4
3862 atoms, 3935 bonds, 4 pseudobonds, 486 residues, 4 models selected
> view matrix models
> #3,0.96671,0.25077,0.050765,-15.154,0.25302,-0.96646,-0.043981,247.55,0.038033,0.055362,-0.99774,284.39
> select add #3
8419 atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 45 models selected
> select subtract #3
4 models selected
> matchmaker #3/b:52-87 to #10/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_in_DDM_chains_renamed_cryo.pdb, chain B (#3), sequence alignment
score = 176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> select #3/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
Alignment identifier is 3/B
> select #10/b
2441 atoms, 2496 bonds, 320 residues, 1 model selected
Alignment identifier is 10/B
> ~select
Nothing selected
> select #3/B:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:9-26
130 atoms, 130 bonds, 18 residues, 1 model selected
> ~select
Nothing selected
> ui tool show "Color Actions"
> ui mousemode right zoom
> cartoon style #3,10 modeHelix tube sides 20
> ui tool show Angles/Torsions
Either three or four atoms must be selected!
> cartoon style #3,10 modeHelix tube sides 20
> cartoon style #3,10 xsection oval modeHelix default
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> hide #!10 models
> hide #!3 models
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_DDM_chains_renamed.pdb
Chain information for MolBC_WT_in_DDM_chains_renamed.pdb #17
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> rename #17 MolBC_WT_in_DDM_chains_renamed_test.pdb
> open
> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc_MolA_deleted.pdb
Chain information for MolABC_no_nuc_MolA_deleted.pdb #18
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> rename #18 MolABC_no_nuc_MolA_deleted_test.pdb
> matchmaker #17/b:52-87 to #18/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted_test.pdb, chain B (#18) with
MolBC_WT_in_DDM_chains_renamed_test.pdb, chain B (#17), sequence alignment
score = 176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> view
> select #18/b
2441 atoms, 2496 bonds, 320 residues, 1 model selected
> color sel blue
> select #18/c
2411 atoms, 2465 bonds, 316 residues, 1 model selected
> color sel cornflower blue
> select #17/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> ui tool show "Color Actions"
> color sel saddle brown
> select #17/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!17 & sel) orange red
> ~select
Nothing selected
> measure rotation #17 toModel #18 showSlabs true
Position of MolBC_WT_in_DDM_chains_renamed_test.pdb #17 relative to
MolABC_no_nuc_MolA_deleted_test.pdb #18 coordinates:
Matrix rotation and translation
0.96671388 0.25077316 0.05076500 -13.12646901
0.25301729 -0.96646153 -0.04398133 247.98830480
0.03803308 0.05536179 -0.99774173 274.25174590
Axis 0.99163829 0.12708940 0.02240077
Axis point 0.00000000 121.37679976 140.36816995
Rotation angle (degrees) 177.12883000
Shift along axis 24.64342675
> hide #!20 models
> hide #20.1 models
> hide #20.2 models
> hide #19 models
> hide #!17 models
> hide #18 models
> show #!12 models
> show #!3 models
> hide #!12 models
> show #!10 models
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select #3/c:194
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #10/c:194
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #10
8850 atoms, 9039 bonds, 1139 residues, 38 models selected
> select subtract #10
Nothing selected
> ui mousemode right "translate selected models"
Either three or four atoms must be selected!
> select #10/c:194
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui mousemode right select
Drag select of 20 atoms, 23 bonds, 1 residues
Either three or four atoms must be selected!
> select #10/c:194
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/c:194
14 atoms, 15 bonds, 1 residue, 1 model selected
Either three or four atoms must be selected!
> ~select
Nothing selected
No atoms selected
> angle
Missing or invalid "objects" argument: empty atom specifier
> select #3.7.29
1 model selected
> select #10.1.29
1 model selected
> angle 3.7.29 to 10.1.29
Missing or invalid "objects" argument: invalid objects specifier
> angle 3.7.29, 10.1.29
Missing or invalid "objects" argument: invalid objects specifier
> angle 3.7.29 10.1.29
Missing or invalid "objects" argument: invalid objects specifier
> angle @3.7.29 @10.1.29
Missing or invalid "objects" argument: only initial part "@3" of atom
specifier valid
> angle @3.7.29, @10.1.29
Missing or invalid "objects" argument: only initial part "@3" of atom
specifier valid
> angle @3.7.29 to @10.1.29
Missing or invalid "objects" argument: only initial part "@3" of atom
specifier valid
Either three or four atoms must be selected!
> angle #3.7.29@ca to #10.1.29@ca
Expected a number or a keyword
> select #3.7.29
1 model selected
chain C helix 9 #3.7.29 to chain C helix 11 #10.1.29: distance: 245.802Å;
angle: 5.6°
> select add #3
8419 atoms, 8591 bonds, 9 pseudobonds, 1084 residues, 43 models selected
> select subtract #3
4 models selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #!3,10 atoms
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view orient
> view
> ui tool show "Side View"
> view
> ui mousemode right zoom
> cartoon style #3,10 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!3 models
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> show #!3 models
> hide #!3 models
> select #10.1.1
1 model selected
> ~select #10.1.1
Nothing selected
> cartoon style #10.1.1#!10#!10.1 xsection oval modeHelix default
> select #10.1.1
1 model selected
> ~select #10.1.1
Nothing selected
> show #!3 models
> cartoon style #3#10.1.2-5#!10#!10.1 xsection oval modeHelix default
> hide #!3 models
> cartoon style #10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 modeHelix tube sides
> 20
> cartoon style #10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 xsection oval
> modeHelix default
> cartoon style #10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 modeHelix tube sides
> 20
> show #!3 models
> cartoon style #3#10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 modeHelix tube sides
> 20
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> cartoon style #3#10.1.2-5,7-11,14-27,29,32-36#!10#!10.1 xsection oval
> modeHelix default
> ui mousemode right "translate selected models"
> ui mousemode right zoom
chain B helix 2 #3.7.2 to chain B helix 2 #10.1.2: distance: 270.676Å; angle:
4.4°
chain B helix 1 #3.7.1 to chain B helix 1 #10.1.1: distance: 242.099Å; angle:
1.7°
> ui mousemode right "translate selected models"
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 21584 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #3/d,e
3862 atoms, 3935 bonds, 5 pseudobonds, 486 residues, 3 models selected
> cartoon hide (#!3 & sel)
> select #10/d,e
3998 atoms, 4078 bonds, 503 residues, 1 model selected
> cartoon hide sel
> cartoon style protein modeHelix default arrows false xsection round width
> 0.2 thickness 0.3
> select add #10
8850 atoms, 9039 bonds, 1139 residues, 38 models selected
> select subtract #10
Nothing selected
> cartoon style #3,10 modeHelix tube sides 20
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> cartoon style #3,10 xsection oval modeHelix default
> cartoon style #3,10 modeHelix tube sides 20
> hide #!10 models
> cartoon style #3 xsection oval modeHelix default
> cartoon style #3 modeHelix tube sides 20
> show #!10 models
> cartoon style #3,10 xsection rectangle modeHelix default
> cartoon style (#3,10 & coil) xsection oval
> cartoon style #3,10 xsection barbell modeHelix default
> cartoon style #3,10 modeHelix tube sides 20
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #!10 models
> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
> show #!10 models
> hide #!3 models
> save /Users/alexandrakaragiaridi/Desktop/image5.png supersample 3
> show #!3 models
> save /Users/alexandrakaragiaridi/Desktop/image6.png supersample 3
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!3 models
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> show #!3 models
> hide #!10 models
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> show #!10 models
> transparency #3 0.5
> transparency #3 0.5 target c
> transparency #3 0.7 target c
> transparency #3 0 target c
> transparency #10 0.5 target c
> transparency #10 0.5 target r
> transparency #10 50 target r
> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
> transparency #10 70 target r
> save /Users/alexandrakaragiaridi/Desktop/image5.png supersample 3
> hide #!3 models
> show #!3 models
> transparency #3 50 target r
> save /Users/alexandrakaragiaridi/Desktop/image6.png supersample 3
> transparency #3 0 target r
> transparency #3=10 0 target r
Missing or invalid "percent" argument: Expected a number
> transparency #10 0 target r
> hide #!3 models
> show #!3 models
> ui mousemode right zoom
> hide #!3 models
> show #!3 models
> transparency #10 0.5 target r
> transparency #10 0 target r
> transparency #10 0.6 target r
> transparency #10 0.7 target r
> transparency #10 70 target r
> transparency #10 50 target r
> transparency #10 0 target r
> transparency #10 70 target r
> transparency #10 0 target r
> cartoon style #3,10 xsection oval modeHelix default
> ui mousemode right "translate selected models"
> ui mousemode right zoom
chain B helix 1 #10.1.1 to chain B helix 1 #3.7.1: distance: 242.099Å; angle:
1.7°
chain B helix 2 #10.1.2 to chain B helix 2 #3.7.2: distance: 270.676Å; angle:
4.4°
> select #3.7.5
1 model selected
> ~select #3.7.5
Nothing selected
> select #10.1.5
1 model selected
> ~select #10.1.5
Nothing selected
chain B helix 5 #3.7.5 to chain B helix 5 #10.1.5: distance: 119.069Å; angle:
2.0°
> select #3.7.3
1 model selected
> select #10.1.4
1 model selected
> select #3.7.3
1 model selected
chain B helix 3 #3.7.3 to chain B helix 4 #10.1.4: distance: 87.665Å; angle:
65.5°
No visible atoms or bonds selected
> ~select #3.7.3
Nothing selected
> cartoon style #3.1-6#3.7.1-5#10.1.1-5#!3,10#!3.7#!10.1 modeHelix tube sides
> 20
> cartoon style #3.1-6#3.7.1-5#10.1.1-5#!3,10#!3.7#!10.1 xsection oval
> modeHelix default
> select #3.7.6
1 model selected
> select #10.1.7
1 model selected
> ~select #10.1.7
Nothing selected
chain B helix 6 #3.7.6 to chain B helix 7 #10.1.7: distance: 250.982Å; angle:
4.0°
> select #3.7.7
1 model selected
> select #10.1.8
1 model selected
chain B helix 8 #10.1.8 to chain B helix 7 #3.7.7: distance: 133.997Å; angle:
0.4°
> ~select #10.1.8
Nothing selected
> cartoon style #3.1-6#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 modeHelix tube
> sides 20
> cartoon style #3.1-6#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 xsection oval
> modeHelix default
> cartoon style #3.1-6#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 modeHelix tube
> sides 20
> ui mousemode right "translate selected models"
value: array([ 0, 150, 255, 255], dtype=uint8) default: None
> define axis #10 perHelix true color #0096ff name test radius 0.2
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 1' centered at
[138.89432873 118.0602333 148.78947106] with direction [-0.03321708
-0.02481161 -0.99914014], radius 0.2, and length 21.8343
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 2' centered at
[137.22470514 119.20230369 134.81783977] with direction [-0.01245078
0.08491942 -0.99631003], radius 0.2, and length 7.63264
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 3' centered at
[138.05372817 108.06764281 128.51475989] with direction [ 0.8026101
-0.59184527 0.07440569], radius 0.2, and length 18.5767
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 4' centered at
[145.72161104 116.33145977 124.84189419] with direction [0.1508822 0.53938742
0.8284297 ], radius 0.2, and length 16.9619
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 5' centered at
[150.81669695 129.65128059 147.93503227] with direction [0.22863824 0.50193185
0.83413966], radius 0.2, and length 38.3494
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 6' centered at
[155.28565702 143.07274943 150.93031609] with direction [0.52188408 0.82517202
0.21616696], radius 0.2, and length 6.46639
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 7' centered at
[161.4682541 142.4935721 136.67182626] with direction [ 0.20901679 -0.00098958
-0.97791155], radius 0.2, and length 21.903
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 8' centered at
[167.8756954 139.366525 144.05325253] with direction [0.21956307 0.43124242
0.87511258], radius 0.2, and length 36.8449
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 9' centered at
[160.91926351 150.94322402 144.77402766] with direction [-0.05428096
0.15150463 -0.98696501], radius 0.2, and length 38.4235
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 10' centered at
[153.16255893 144.72955059 127.98594293] with direction [-0.39611073
-0.47095447 0.7882247 ], radius 0.2, and length 12.3565
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 11' centered at
[159.05351081 123.17544409 145.89835395] with direction [0.04832853 0.00678212
0.99880847], radius 0.2, and length 30.5075
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 12' centered at
[156.62467727 129.23983617 166.64295286] with direction [-0.60476875
0.72433613 0.33104672], radius 0.2, and length 5.7345
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 13' centered at
[157.41472133 133.74646525 168.35308858] with direction [ 0.28281302
-0.91915742 0.27416498], radius 0.2, and length 5.7588
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 14' centered at
[163.09860358 136.86333389 175.22680129] with direction [ 0.34520149
-0.79444064 0.49969992], radius 0.2, and length 10.8468
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 15' centered at
[161.69075667 133.55055861 150.55871106] with direction [-0.36743289
-0.02621678 -0.92968046], radius 0.2, and length 32.6292
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 16' centered at
[141.58698056 132.34284382 157.58710316] with direction [-0.29675497 -0.608367
0.73608836], radius 0.2, and length 15.2808
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 17' centered at
[143.12102326 127.70175984 146.94348142] with direction [-0.3506446 0.18488988
-0.9180763 ], radius 0.2, and length 37.8351
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain B helix 18' centered at
[138.4415738 140.61248037 144.71229819] with direction [-0.44904978 0.15017058
0.88079685], radius 0.2, and length 22.7906
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 1' centered at
[163.29064596 182.64512887 148.75598259] with direction [-0.05834301
0.00278421 0.99829271], radius 0.2, and length 21.7356
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 2' centered at
[165.21133484 181.2794909 134.90715963] with direction [-0.06092366 0.07495203
0.99532432], radius 0.2, and length 7.38453
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 3' centered at
[164.53561146 192.4729011 128.65578467] with direction [-0.81244329 0.5813858
0.04389144], radius 0.2, and length 18.5121
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 4' centered at
[157.45680002 184.37817105 123.8528681 ] with direction [-0.32193823
-0.50009725 0.80390206], radius 0.2, and length 14.3044
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 5' centered at
[151.36637968 172.18926675 146.45943825] with direction [-0.2624205
-0.46650916 0.84469206], radius 0.2, and length 38.9625
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 6' centered at
[139.79168852 158.62661407 136.63319875] with direction [-0.20785876
-0.01337435 -0.97806741], radius 0.2, and length 21.8971
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 7' centered at
[133.6554324 161.4499327 144.85609143] with direction [-0.24901695 -0.43824913
0.86367139], radius 0.2, and length 28.8519
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 8' centered at
[140.13677409 149.89764288 143.42844734] with direction [ 0.05595601
-0.15755276 -0.98592396], radius 0.2, and length 35.6621
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 9' centered at
[148.28963686 155.95675428 127.59072569] with direction [0.45002321 0.52608488
0.72160503], radius 0.2, and length 9.98349
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 10' centered at
[150.0577348 159.38419006 133.64248285] with direction [ 0.65314182
-0.01925877 0.75699066], radius 0.2, and length 5.7923
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 11' centered at
[142.89437046 178.30495372 145.65238848] with direction [-0.06655957
-0.00993754 0.99773296], radius 0.2, and length 30.3111
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 12' centered at
[144.66131052 173.82859124 165.72848631] with direction [-0.12653854
-0.9912196 -0.03836286], radius 0.2, and length 5.90297
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 13' centered at
[143.98287464 167.83074192 168.24932632] with direction [-0.27621718
0.93078782 0.23945377], radius 0.2, and length 5.71805
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 14' centered at
[138.04156465 165.70742773 175.38542078] with direction [-0.22092881
0.89691282 0.38306377], radius 0.2, and length 11.423
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 15' centered at
[139.6405478 167.88023035 151.11277642] with direction [ 0.3546893 0.01839823
-0.93480319], radius 0.2, and length 34.6455
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 16' centered at
[160.210276 168.69872157 158.12497637] with direction [0.49255082 0.48463911
0.7228545 ], radius 0.2, and length 12.405
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 17' centered at
[158.65506626 173.21794452 146.9061338 ] with direction [ 0.34973132
-0.20483791 -0.91418239], radius 0.2, and length 37.8498
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain C helix 18' centered at
[161.04181351 161.02595429 140.82768715] with direction [ 0.62687875
-0.11819244 0.77009972], radius 0.2, and length 14.1207
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 1' centered at
[168.76700144 141.7958998 185.53240035] with direction [ 0.41814452
-0.85006236 -0.32023295], radius 0.2, and length 14.3046
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 2' centered at
[148.24594739 127.49258116 176.58352434] with direction [ 0.94351814
0.14475109 -0.29802793], radius 0.2, and length 5.90175
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 3' centered at
[155.45300825 125.8189693 177.34230037] with direction [ 0.94930299
-0.28394858 -0.13489639], radius 0.2, and length 10.0409
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 4' centered at
[151.10493761 119.20162945 182.35952123] with direction [-0.37011828
0.49951086 0.78326328], radius 0.2, and length 14.4107
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 5' centered at
[147.40439667 123.05661258 190.19266188] with direction [-0.00875559
-0.79589813 -0.60536725], radius 0.2, and length 5.44482
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 6' centered at
[141.57140032 136.12936891 177.8823915 ] with direction [-0.77937561 0.4911306
0.38905578], radius 0.2, and length 5.93556
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 7' centered at
[149.95074934 133.06815503 185.7198464 ] with direction [ 0.74252233
-0.64996276 -0.16189194], radius 0.2, and length 18.616
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 8' centered at
[157.89141083 124.64099433 184.3669659 ] with direction [ 0.63240665
-0.47596771 -0.61116002], radius 0.2, and length 6.00605
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 9' centered at
[151.32947596 133.32780545 197.91343184] with direction [ 0.71144945
-0.68998224 0.13328237], radius 0.2, and length 24.2622
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 10' centered at
[157.32927478 142.29031805 203.75612885] with direction [ 0.08528956
-0.98386135 0.15729762], radius 0.2, and length 11.4332
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 11' centered at
[167.45280133 143.21626877 209.07861051] with direction [ 0.51964799
0.85435156 -0.00702718], radius 0.2, and length 5.78006
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain D helix 12' centered at
[165.55567951 155.12922861 205.26760417] with direction [ 0.14497464
-0.39113787 0.90884186], radius 0.2, and length 12.0269
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 1' centered at
[133.39473484 157.07146631 185.87999495] with direction [-0.39860215
0.88157301 -0.2528742 ], radius 0.2, and length 19.4134
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 2' centered at
[153.07830876 173.80337272 176.46874051] with direction [-0.94017596
-0.14546857 -0.30807153], radius 0.2, and length 6.02798
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 3' centered at
[146.70080408 175.02852424 177.22092458] with direction [-9.91926295e-01
3.33135128e-04 -1.26815273e-01], radius 0.2, and length 7.52775
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 4' centered at
[150.481171 182.85501584 182.3381486 ] with direction [ 0.32582667 -0.48308072
0.81269306], radius 0.2, and length 20.9936
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 5' centered at
[160.68109744 176.30491972 183.96304867] with direction [ 0.24314391
-0.60924617 -0.75478484], radius 0.2, and length 6.12268
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 6' centered at
[159.7829355 165.1504365 177.91728631] with direction [ 0.80732077 -0.4232423
0.41121665], radius 0.2, and length 5.72695
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 7' centered at
[151.26069892 168.44683323 185.62348711] with direction [-0.73463437
0.65423124 -0.17970486], radius 0.2, and length 18.5879
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 8' centered at
[143.49635171 176.86572021 184.07650532] with direction [-0.61488979
0.45748837 -0.6423511 ], radius 0.2, and length 5.84625
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 9' centered at
[149.7592522 168.1814334 197.81316584] with direction [-0.71101184 0.69313967
0.11840424], radius 0.2, and length 24.3445
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 10' centered at
[143.7666456 159.45212789 203.61703639] with direction [ 0.08102842
-0.98798961 -0.13157097], radius 0.2, and length 11.5155
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 11' centered at
[133.80269407 159.30297004 209.29743794] with direction [-0.52713162
-0.58705225 0.61441184], radius 0.2, and length 5.77119
Axis 'MolABC_no_nuc_MolA_deleted.pdb #10/test/chain E helix 12' centered at
[135.3884304 146.52843308 205.04864675] with direction [-0.12217055 0.41913337
0.89966748], radius 0.2, and length 11.9003
> cartoon style #3.1-6#10.2#3.7.1-7#10.1.1-5,7-8#!3,10#!3.7#!10.1 xsection
> oval modeHelix default
chain B helix 1 #10.2.1 to chain B helix 2 #10.2.2: distance: 1.672Å; angle:
6.4°
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> close #10.2.1-60
chain E helix 11 to chain E helix 12: distance: 7.725Å; angle: 68.2°
> select #10.1.8
1 model selected
> select #3.7.7
1 model selected
chain B helix 7 #3.7.7 to chain B helix 8 #10.1.8: distance: 133.997Å; angle:
0.4°
> ~select #3.7.7
Nothing selected
> select #3.7.8
1 model selected
> select #10.1.9
1 model selected
chain B helix 8 #3.7.8 to chain B helix 9 #10.1.9: distance: 286.501Å; angle:
1.5°
> ~select #10.1.9
Nothing selected
> select #3.7.9
1 model selected
> select #10.1.10
1 model selected
chain B helix 9 #3.7.9 to chain B helix 10 #10.1.10: distance: 348.095Å;
angle: 10.4°
> ~select #10.1.10
Nothing selected
> select #3.7.12
1 model selected
> ~select #3.7.12
Nothing selected
> select #3.7.11
1 model selected
> select #10.1.11
1 model selected
> select #3.7.11
1 model selected
> ~select #3.7.11
Nothing selected
> select #10.1.11
1 model selected
> ~select #10.1.11
Nothing selected
chain B helix 11 #10.1.11 to chain B helix 11 #3.7.11: distance: 235.684Å;
angle: 10.5°
> select #10.1.11
1 model selected
> ~select #10.1.11
Nothing selected
> select #3.7.11
1 model selected
> ~select #3.7.11
Nothing selected
chain B helix 11 #3.7.11 to chain B helix 11 #10.1.11: distance: 235.684Å;
angle: 10.5°
> select #3.7.16
1 model selected
> select #10.1.15
1 model selected
chain B helix 16 #3.7.16 to chain B helix 15 #10.1.15: distance: 263.346Å;
angle: 0.8°
> select #10.1.16
1 model selected
> select #3.7.17
1 model selected
chain B helix 17 #3.7.17 to chain B helix 16 #10.1.16: distance: 326.486Å;
angle: 43.0°
> ~select #3.7.17
Nothing selected
> select #3.7.19
1 model selected
> select #10.1.17
1 model selected
chain B helix 17 #10.1.17 to chain B helix 19 #3.7.19: distance: 310.377Å;
angle: 0.7°
> ~select #10.1.17
Nothing selected
> select #3.7.20
1 model selected
> select #10.1.18
1 model selected
> ~select #10.1.18
Nothing selected
chain B helix 20 #3.7.20 to chain B helix 18 #10.1.18: distance: 235.004Å;
angle: 0.9°
> select #3.7.21
1 model selected
> select #10.1.19
1 model selected
chain C helix 1 #3.7.21 to chain C helix 1 #10.1.19: distance: 230.089Å;
angle: 7.1°
> ~select #10.1.19
Nothing selected
> select #10.1.20
1 model selected
> select #3.7.22
1 model selected
chain C helix 2 #3.7.22 to chain C helix 2 #10.1.20: distance: 217.796Å;
angle: 7.6°
> ~select #3.7.22
Nothing selected
> select #10.1.23
1 model selected
> select #10.1.22
1 model selected
> ~select #10.1.22
Nothing selected
> select #10.1.21
1 model selected
> ~select #10.1.21
Nothing selected
> select #3.7.23
1 model selected
> select #10.1.23
1 model selected
chain C helix 5 #10.1.23 to chain C helix 3 #3.7.23: distance: 350.237Å;
angle: 1.7°
> select #10.1.21
1 model selected
> ~select #10.1.21
Nothing selected
> select #3.7.24
1 model selected
> select #10.1.24
1 model selected
chain C helix 4 #3.7.24 to chain C helix 6 #10.1.24: distance: 242.240Å;
angle: 2.6°
> select #3.7.24
1 model selected
> ~select #3.7.24
Nothing selected
> select #3.7.25
1 model selected
> select #10.1.25
1 model selected
chain C helix 7 #10.1.25 to chain C helix 5 #3.7.25: distance: 343.916Å;
angle: 1.2°
> ~select #10.1.25
Nothing selected
> select #3.7.26
1 model selected
> select #10.1.26
1 model selected
chain C helix 6 #3.7.26 to chain C helix 8 #10.1.26: distance: 190.730Å;
angle: 3.0°
> ~select #10.1.26
Nothing selected
> select #3.7.26
1 model selected
> ~select #3.7.26
Nothing selected
> select #10.1.27
1 model selected
> select #3.7.26
1 model selected
> select #10.1.26
1 model selected
> select #3.7.25
1 model selected
> select #3.7.24
1 model selected
> ~select #3.7.24
Nothing selected
> select #10.1.27
1 model selected
> select #3.7.27
1 model selected
chain C helix 7 #3.7.27 to chain C helix 9 #10.1.27: distance: 182.312Å;
angle: 18.3°
> view matrix models
> #3.7.27,1,3.4694e-17,1.3878e-17,6.0475,4.3672e-16,1,-6.9389e-17,-7.7937,-1.3878e-17,1.3878e-17,1,4.0305
> ~select #3.7.27
Nothing selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> cartoon #3.1-6#10.2#!3,10#!3.7#!10.1
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #!10 models
> select #3/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!3 & sel) blue
> select #3/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!3 & sel) cornflower blue
> select #3/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> color (#!3 & sel) purple
> select #3/e
1977 atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolBC_WT_in_DDM.json
Opened 1 Mole channels in MolBC_WT_in_DDM_chains_renamed.pdb
> hide #!3 models
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_DDM_chains_renamed.pdb
Chain information for MolBC_WT_in_DDM_chains_renamed.pdb #22
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> ui mousemode right zoom
> close #3
> select #22/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!22 & sel) blue
> select #22/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!22 & sel) cornflower blue
> select #22/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> color (#!22 & sel) purple
> select #22/e
1977 atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> hide #22
> cartoon style width .5 thickness .5
> set bgColor light cyan
> cartoon style width .5 thickness .5
> graphics silhouettes true depthJump .01
> camera ortho
> select #21 & @@radius<2
20 atoms, 20 residues, 1 model selected
> show protein & sel :<2.5
> size stickRadius .4
Changed 152134 bond radii
> ~select
Nothing selected
> cartoon suppressBackboneDisplay false
> surface #21
> hide #21
> color byattribute radius #21 palette puor key true
> key puor :0.98 :2.09 :3.20 :4.32 :5.43 showTool true
> ui mousemode right "color key"
332 atoms, 332 residues, 1 surfaces, atom radius range 0.975 to 5.43
> ui mousemode right zoom
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> ui mousemode right "color key"
> key pos 0.282674,0.137575 size 0.30482,0.05151
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #!21 models
> hide #!21.1 models
> hide #!22 models
> hide #3 models
> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolBC_WT_in_DM.json
Opened 1 Mole channels in MolBC_WT_in_DM_chains_renamed.pdb
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_DM_chains_renamed.pdb
Chain information for MolBC_WT_in_DM_chains_renamed.pdb #24
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> close #1
> select #24/b
2489 atoms, 2398 bonds, 2 pseudobonds, 450 residues, 2 models selected
> color (#!24 & sel) blue
> select #24/c
2420 atoms, 2305 bonds, 2 pseudobonds, 462 residues, 2 models selected
> color (#!24 & sel) cornflower blue
> select #24/d
2165 atoms, 2035 bonds, 421 residues, 1 model selected
> color sel purple
> select #24/e
2175 atoms, 2005 bonds, 1 pseudobond, 456 residues, 2 models selected
> ui tool show "Color Actions"
> color sel violet
> select add #24
9249 atoms, 8743 bonds, 5 pseudobonds, 1789 residues, 2 models selected
> select subtract #24
Nothing selected
> hide #24
> cartoon style width .5 thickness .5
> graphics silhouettes true depthJump .01
> camera ortho
> select #23 & @@radius<2
43 atoms, 43 residues, 1 model selected
> show protein & sel :<2.5
> size stickRadius .4
Changed 152134 bond radii
> ~select
Nothing selected
> cartoon suppressBackboneDisplay false
> surface #23
> hide #23
> color byattribute radius #23 palette puor key true
> key puor :0.79 :2.33 :3.87 :5.41 :6.95 showTool true
367 atoms, 367 residues, 1 surfaces, atom radius range 0.793 to 6.95
> show #3 models
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> hide #!23 models
> hide #!23.1 models
> hide #!24 models
> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolBC_WT_in_C5.json
Opened 1 Mole channels in MolBC_WT_in_C5_chains_renamed.pdb
> view
> close #5
> open
> /Users/alexandrakaragiaridi/Desktop/MolBC_WT_cryo_EM_structure/MolBC_WT_in_C5_chains_renamed.pdb
Chain information for MolBC_WT_in_C5_chains_renamed.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> select subtract #4
Nothing selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select #5/b
2354 atoms, 2405 bonds, 2 pseudobonds, 309 residues, 2 models selected
> color (#!5 & sel) blue
> select #5/c
2304 atoms, 2353 bonds, 2 pseudobonds, 303 residues, 2 models selected
> color (#!5 & sel) cornflower blue
> select #5/d
1996 atoms, 2036 bonds, 251 residues, 1 model selected
> color sel purple
> select #5/e
2004 atoms, 2044 bonds, 252 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> hide #5
> cartoon style width .5 thickness .5
> select add #5
8692 atoms, 8874 bonds, 4 pseudobonds, 1116 residues, 2 models selected
> select subtract #5
Nothing selected
> cartoon style width .5 thickness .5
> graphics silhouettes true depthJump .01
> camera ortho
> select #1 & @@radius<2
60 atoms, 60 residues, 1 model selected
> show protein & sel :<2.5
> size stickRadius .4
Changed 152134 bond radii
> ~select
Nothing selected
> cartoon suppressBackboneDisplay false
> surface #1
> hide #1
> color byattribute radius #1 palette puor
287 atoms, 287 residues, 1 surfaces, atom radius range 0.869 to 6.09
> color byattribute radius #1 palette puor key true
> key puor :0.87 :2.17 :3.48 :4.79 :6.09 showTool true
287 atoms, 287 residues, 1 surfaces, atom radius range 0.869 to 6.09
> ui mousemode right "rotate selected models"
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #!5 models
> hide #!1 models
> hide #!1.1 models
> open /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_WT_in_DDM.json
Opened 1 Mole channels in MolABC_no_nuc.pdb
> open
> /Users/alexandrakaragiaridi/Desktop/MolABC_no_nuc_everything/MolABC_no_nuc.pdb
Chain information for MolABC_no_nuc.pdb #26
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> view
> close #7
> hide #25.1#!26 atoms
> show #25.1#!26 cartoons
> show #25.1#!26 atoms
> select add #26
11335 atoms, 11571 bonds, 1 pseudobond, 1452 residues, 2 models selected
> hide sel atoms
> select subtract #26
Nothing selected
> select subtract #4
Nothing selected
> ui mousemode right "translate selected models"
> select #26/a
2485 atoms, 2532 bonds, 1 pseudobond, 313 residues, 2 models selected
> color (#!26 & sel) orange
> select #26/
Expected an objects specifier or a keyword
> select #26/b
2441 atoms, 2496 bonds, 320 residues, 1 model selected
> color sel blue
> select #26/c
2411 atoms, 2465 bonds, 316 residues, 1 model selected
> color sel cornflower blue
> select #26/d
2003 atoms, 2043 bonds, 252 residues, 1 model selected
> color sel purple
> select #26/e
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> hide #26
> cartoon style width .5 thickness .5
> graphics silhouettes true depthJump .01
> camera ortho
> select #25 & @@radius<2
22 atoms, 22 residues, 1 model selected
> show protein & sel :<2.5
> size stickRadius .4
Changed 152134 bond radii
> ~select
Nothing selected
> cartoon suppressBackboneDisplay false
> surface #25
> hide #25
> color byattribute radius #25 palette puor
325 atoms, 325 residues, 1 surfaces, atom radius range 0.987 to 4.92
> color byattribute radius #25 palette puor key true
> key puor :0.99 :1.97 :2.96 :3.94 :4.92 showTool true
325 atoms, 325 residues, 1 surfaces, atom radius range 0.987 to 4.92
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #!25 models
> hide #!25.1 models
> hide #!26 models
> open
> /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_E154Q_AMPPNP_in_DDM.json
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/__init__.py", line 27, in open
return mole.read_mole_json(session, data, file_name, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 44, in read_mole_json
models = channel_models(session, j['Channels'], transparency/100.0)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mole/mole.py", line 83, in channel_models
ms.create_marker((x,y,z), color, r)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/markers/markers.py", line 26, in create_marker
a.radius = radius
File "atomic_cpp/cymol.pyx", line 456, in
chimerax.atomic.cymol.CyAtom.radius.__set__
RuntimeError: radius must be positive
RuntimeError: radius must be positive
File "atomic_cpp/cymol.pyx", line 456, in
chimerax.atomic.cymol.CyAtom.radius.__set__
See log for complete Python traceback.
> open
> /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_E154Q_AMPPNP_in_DDM_MolA_deleted.json
Opened 1 Mole channels in MolABC_nuc_MolA_deleted.pdb
> open "/Users/alexandrakaragiaridi/Desktop/MolABC_nuc_everything/yes
> SBP/MolABC_nuc_MolA_deleted.pdb"
Chain information for MolABC_nuc_MolA_deleted.pdb #27
---
Chain | Description
B | No description available
C | No description available
D E | No description available
> close #12
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select #27/b
2278 atoms, 2327 bonds, 1 pseudobond, 299 residues, 2 models selected
> color (#!27 & sel) blue
> select #27/c
2494 atoms, 2550 bonds, 326 residues, 1 model selected
> color sel cornflower blue
> select #27/d
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> color sel purple
> select #27/e
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> ui hideFloating toggle
> ~select
Nothing selected
> select ::name="ANP"
176 atoms, 184 bonds, 4 residues, 2 models selected
> color (#!27 & sel) forest green
> ~select
Nothing selected
> hide #27
> show #27
> hide #7.1#!27 atoms
> select ::name="ANP"
176 atoms, 184 bonds, 4 residues, 2 models selected
> show sel & #!27 atoms
> ~select
Nothing selected
> cartoon style width .5 thickness .5
> graphics silhouettes true depthJump .01
> camera ortho
> select #7 & @@radius<2
88 atoms, 88 residues, 1 model selected
> show sel atoms
> close #7
> open
> /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_E154Q_AMPPNP_in_DDM_MolA_deleted.json
Opened 1 Mole channels in MolABC_nuc_MolA_deleted.pdb
> select #7 & @@radius<2
88 atoms, 88 residues, 1 model selected
> show protein & sel :<2.5
> size stickRadius .4
Changed 152134 bond radii
> ~select
Nothing selected
> cartoon suppressBackboneDisplay false
> surface #7
> hide #7
> color byattribute radius #7 palette puor
356 atoms, 356 residues, 1 surfaces, atom radius range 0.273 to 5.05
> color byattribute radius #7 palette puor key true
> key puor :0.27 :1.47 :2.66 :3.85 :5.05 showTool true
356 atoms, 356 residues, 1 surfaces, atom radius range 0.273 to 5.05
> select subtract #4
Nothing selected
> ui mousemode right "color key"
> key pos 0.288138,0.30604 size 0.307849,0.0510151
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> ui mousemode right zoom
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> hide #!7 models
> hide #!7.1 models
> hide #!27 models
> open
> /Users/alexandrakaragiaridi/Desktop/Pore_for_MolBC_E154Q_AMPPNP_in_DDM_MolA_not_resolved.json
Opened 1 Mole channels in MolBC_nuc.pdb
> open "/Users/alexandrakaragiaridi/Desktop/MolABC_nuc_everything/no
> SBP/MolBC_nuc.pdb"
Chain information for MolBC_nuc.pdb #28
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
> ui mousemode right "translate selected models"
> select #28/b
2218 atoms, 2265 bonds, 1 pseudobond, 292 residues, 2 models selected
> color (#!28 & sel) blue
> select #28/c
2193 atoms, 2240 bonds, 1 pseudobond, 288 residues, 2 models selected
> color (#!28 & sel) cornflower blue
> select #28/d
1995 atoms, 2035 bonds, 251 residues, 1 model selected
> color sel purple
> select #28/e
2004 atoms, 2044 bonds, 252 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> ~select
Nothing selected
> select ::name="ANP"
264 atoms, 276 bonds, 6 residues, 3 models selected
> color (#!28 & sel) forest green
> cartoon style width .5 thickness .5
> ~select
Nothing selected
> graphics silhouettes true depthJump .01
> camera ortho
> select #12 & @@radius<2
63 atoms, 63 residues, 1 model selected
> show protein & sel :<2.5
> size stickRadius .4
Changed 160810 bond radii
> ~select
Nothing selected
> cartoon suppressBackboneDisplay false
> surface #12
> hide #12
> color byattribute radius #12 palette puor key true
> key puor :0.07 :1.43 :2.78 :4.14 :5.49 showTool true
269 atoms, 269 residues, 1 surfaces, atom radius range 0.072 to 5.49
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> hide #!12 models
> hide #!12.1 models
> hide #!28 models
> show #!22 models
> show #!21 models
> show #!21.1 models
> view
> color byattribute radius #21 palette puor key true
> key puor :0.98 :2.09 :3.20 :4.32 :5.43 showTool true
332 atoms, 332 residues, 1 surfaces, atom radius range 0.975 to 5.43
> ui mousemode right "color key"
> key pos 0.237292,0.0158719 size 0.338266,0.0439568
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "color key"
> key pos 0.288773,0.112881 size 0.3318,0.0549079
> key pos 0.349599,0.0976512 size 0.292846,0.0648739
> ui mousemode right "translate selected models"
> select add #22
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 2 models selected
> show sel surfaces
> hide sel cartoons
> transparency (#!22 & sel) 50
> transparency (#!22 & sel) 70
> hide sel atoms
> hide sel cartoons
> select subtract #22
4 models selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui tool show "Side View"
> hide #!21.1 models
> show #!21.1 models
> hide #!21 models
> show #!21 models
> select add #21
332 atoms, 332 residues, 2 models selected
> select subtract #21.1
2 models selected
> select add #21.1
332 atoms, 332 residues, 2 models selected
> show sel atoms
> select subtract #21.1
2 models selected
> select add #21
332 atoms, 332 residues, 2 models selected
> select subtract #21
1 model selected
> select add #21
332 atoms, 332 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> surface #21
> hide #21
> select subtract #21
1 model selected
> hide #!21.1.1 models
> show #21.1.1 models
> color #21.1.1 #0096ffff
> color byattribute radius #21 palette puor
332 atoms, 332 residues, 1 surfaces, atom radius range 0.975 to 5.43
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "color key"
> key pos 0.321208,0.0202819 size 0.32441,0.0573437
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "color key"
> key pos 0.32751,0.0590548 size 0.325979,0.0579122
> ui mousemode right "translate selected models"
> select #22/b:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> cartoon (#!22 & sel)
> select #22/c:147-186
315 atoms, 320 bonds, 40 residues, 1 model selected
> cartoon (#!22 & sel)
> ~select
Nothing selected
> show protein & sel :<2.5
> show protein & sel :<2
> show protein & sel :<1.5
> show protein & sel :<1
> show protein & sel :<0.5
> select #22/b:95,155,162,259,262
44 atoms, 42 bonds, 5 residues, 1 model selected
> show sel atoms
> select #22/c:95,155,158,162,166
36 atoms, 32 bonds, 5 residues, 1 model selected
> show sel atoms
> ~select
Nothing selected
> select #22/b,c
4557 atoms, 4656 bonds, 4 pseudobonds, 598 residues, 2 models selected
Alignment identifier is 22/B
Alignment identifier is 22/C
> ~select
Nothing selected
> select #22/B:87
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #22/B:87-98
97 atoms, 100 bonds, 12 residues, 1 model selected
> show sel cartoons
> select #22/B:99-100
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #22/B:99-100
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #22/B:99
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #22/B:99-141
325 atoms, 335 bonds, 43 residues, 1 model selected
> show sel cartoons
> select #22/B:142
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #22/B:142-171
226 atoms, 227 bonds, 1 pseudobond, 29 residues, 2 models selected
> show sel cartoons
> ~select
Nothing selected
> select #22/B:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:117-148
252 atoms, 258 bonds, 1 pseudobond, 31 residues, 2 models selected
> hide sel cartoons
> ~select
Nothing selected
> select #22/B:98
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:53-98
346 atoms, 351 bonds, 46 residues, 1 model selected
> show sel cartoons
> ~select
Nothing selected
> select #22/B:114
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:114-116
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #22/B:187
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #22/B:187-208
181 atoms, 188 bonds, 22 residues, 1 model selected
> show sel cartoons
> ~select
Nothing selected
> hide #!22#!21.1 cartoons
> select #22/B:54
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/B:54-113
443 atoms, 451 bonds, 60 residues, 1 model selected
> show sel cartoons
> ~select
Nothing selected
> hide #!22#!21.1 surfaces
> show #!22#!21.1 surfaces
> select add #22
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 10 models selected
> hide sel surfaces
> select subtract #22
4 models selected
> select #22/B:114-115
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #22/B:114-193
619 atoms, 633 bonds, 1 pseudobond, 79 residues, 2 models selected
> show sel cartoons
> ~select
Nothing selected
> select #22/B:194
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #22/B:194-195
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #22/B:187-188
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #22/B:187-213
217 atoms, 224 bonds, 27 residues, 1 model selected
> show sel cartoons
> select #22/B:214
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/B:214-328
862 atoms, 878 bonds, 115 residues, 1 model selected
> show sel cartoons
> ~select
Nothing selected
> cartoon #3,21-22
> save /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
——— End of log from Wed Apr 9 09:24:04 2025 ———
opened ChimeraX session
> ui mousemode right zoom
> hide #3 models
> select subtract #4
Nothing selected
> hide #!21 models
> hide #!21.1 models
> hide #!22 models
> select subtract #4
Nothing selected
> show #!22 models
> hide #!22 atoms
> show #!26 models
> hide #!26 models
> show #!10 models
> matchmaker #22/b:52-87 to #10/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain B (#22), sequence alignment score =
176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> ui mousemode right "translate selected models"
> view
> ui mousemode right "rotate selected models"
> select #22/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> color (#!22 & sel) orange red
> select #22/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!22 & sel) forest green
> select #22/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> select #22/b
2323 atoms, 2374 bonds, 2 pseudobonds, 304 residues, 2 models selected
> crystalcontacts
6 pairs of asymmetric units of 1l7v - BtuCD.pdb contact at distance 3.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
9 0 1 1 0 2 0 1
8 0 1 1 -1 2 0 1
3 0 1 2 -1 1 0 1
3 0 0 0 0 1 0 1
3 0 0 0 0 -1 0 1
2 0 1 2 0 1 0 1
No unit cell parameters for Morph -
MolBC_WT_final_structure_chains_renamed.pdb
> select add #22
8419 atoms, 8591 bonds, 8 pseudobonds, 1084 residues, 3 models selected
> select subtract #22
4 models selected
> hide #!29 models
> select subtract #4
Nothing selected
> view
> select #22/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!22 & sel) dark gray
> select #22/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> select #22/c
2234 atoms, 2282 bonds, 2 pseudobonds, 294 residues, 2 models selected
> color (#!22 & sel) black
> select #22/d
1885 atoms, 1919 bonds, 3 pseudobonds, 238 residues, 2 models selected
> color (#!22 & sel) yellow
> select #22/e
1977 atoms, 2016 bonds, 1 pseudobond, 248 residues, 2 models selected
> color (#!22 & sel) dim gray
> ~select
Nothing selected
> close #6
> close #9
> close #11
> close #13
> close #14
> close #15
> close #16
> close #29
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> morph #22,10, frames 60
Missing or invalid "structures" argument: only initial part "#22,10" of atom
specifier valid
> morph #22,10 frames 60
Computed 61 frame morph #6
> coordset #6 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> morph #10,22 frames 60
Computed 61 frame morph #9
> coordset #9 1,61
> hide #!6 models
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!9 models
> show #!22 models
> show #!10 models
> cartoon style #22#10.2#!10#!10.1 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> cartoon style #22#10.2#!10#!10.1 xsection oval modeHelix default
> matchmaker #22/c:52-87 to #10/c:52-87 60
Expected a keyword
> matchmaker #22/c:52-87 to #10/c:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain C (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain C (#22), sequence alignment score =
144.1
RMSD between 34 pruned atom pairs is 0.463 angstroms; (across all 36 pairs:
1.176)
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> cartoon style #22#10.2#!10#!10.1 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
> cartoon style #22#10.2#!10#!10.1 xsection oval modeHelix default
> morph #10,22 frames 60
Computed 61 frame morph #11
> coordset #11 1,61
> close #11
> close #9
> close #6
> show #!10 models
> show #!22 models
> matchmaker #22/b:52-87 to #10/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain B (#22), sequence alignment score =
176.5
RMSD between 34 pruned atom pairs is 0.581 angstroms; (across all 36 pairs:
1.157)
> morph #10,22 frames 60
Computed 61 frame morph #6
> coordset #6 1,61
> hide #!6 models
> show #!10 models
> show #!22 models
> matchmaker #22/c:52-87 to #10/c:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain C (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain C (#22), sequence alignment score =
144.1
RMSD between 34 pruned atom pairs is 0.463 angstroms; (across all 36 pairs:
1.176)
> morph #10,22 frames 60
Computed 61 frame morph #9
> coordset #9 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!9 models
> show #!22 models
> show #!10 models
> morph #22,10 frames 60
Computed 61 frame morph #11
> coordset #11 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!11 models
> show #!10 models
> show #!22 models
> matchmaker #22/d to #10/d
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain D (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain D (#22), sequence alignment score =
1151.5
RMSD between 236 pruned atom pairs is 0.388 angstroms; (across all 238 pairs:
0.667)
> save /Users/alexandrakaragiaridi/Desktop/image5.png supersample 3
> cartoon style #22#10.2#!10#!10.1 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image6.png supersample 3
> morph #22,10 frames 60
Computed 61 frame morph #13
> coordset #13 1,61
> cartoon style #13 xsection oval modeHelix default
> close #13
> show #!10 models
> show #!22 models
> cartoon style #22#10.2#!10#!10.1 xsection oval modeHelix default
> morph #22,10 frames 60
Computed 61 frame morph #13
> coordset #13 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!13 models
> show #!10 models
> show #!22 models
> morph #10,22 frames 60
Computed 61 frame morph #14
> coordset #14 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!14 models
> show #!10 models
> show #!22 models
> matchmaker #22/e to #10/e
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain E (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain E (#22), sequence alignment score =
1208.5
RMSD between 248 pruned atom pairs is 0.392 angstroms; (across all 248 pairs:
0.392)
> save /Users/alexandrakaragiaridi/Desktop/image7.png supersample 3
> cartoon style #22#10.2#!10#!10.1 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image8.png supersample 3
> cartoon style #22#10.2#!10#!10.1 xsection oval modeHelix default
> morph #22,10 frames 60
Computed 61 frame morph #15
> coordset #15 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!15 models
> show #!10 models
> show #!22 models
> morph #10,22 frames 60
Computed 61 frame morph #16
> coordset #16 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> save /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
——— End of log from Thu Apr 10 14:34:42 2025 ———
opened ChimeraX session
> hide #!16 models
> show #!22 models
> close #18
> close #17
> show #!27 models
> matchmaker #22/e to #27/e
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_MolA_deleted.pdb, chain E (#27) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain E (#22), sequence alignment score =
1204.9
RMSD between 173 pruned atom pairs is 0.770 angstroms; (across all 248 pairs:
1.987)
> view
> ui mousemode right "rotate selected models"
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> cartoon style #22,27 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> cartoon style #22,27 xsection oval modeHelix default
> morph #27,22 frames 60
Computed 61 frame morph #17
> coordset #17 1,61
> hide #!17 atoms
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!17 models
> show #!22 models
> show #!27 models
> morph #22,27 frames 60
Computed 61 frame morph #18
> coordset #18 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> save /Users/alexandrakaragiaridi/Desktop/040325_analysis.cxs
> hide #!18 models
> show #!22 models
> show #!27 models
> matchmaker #22/d to #27/d
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_MolA_deleted.pdb, chain D (#27) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain D (#22), sequence alignment score =
1138.3
RMSD between 162 pruned atom pairs is 0.708 angstroms; (across all 238 pairs:
2.106)
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> cartoon style #22,27 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
> cartoon style #22,27 xsection oval modeHelix default
> morph #22,27 frames 60
Computed 61 frame morph #29
> coordset #29 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!29 models
> morph #27,22 frames 60
Computed 61 frame morph #30
> coordset #30 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!30 models
> show #!27 models
> show #!22 models
> matchmaker #22/E to #27/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_MolA_deleted.pdb, chain E (#27) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain E (#22), sequence alignment score =
1204.9
RMSD between 173 pruned atom pairs is 0.770 angstroms; (across all 248 pairs:
1.987)
> matchmaker #22/D to #27/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_MolA_deleted.pdb, chain D (#27) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain D (#22), sequence alignment score =
1138.3
RMSD between 162 pruned atom pairs is 0.708 angstroms; (across all 238 pairs:
2.106)
> matchmaker #22/c:52-87 to #27/c:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_MolA_deleted.pdb, chain C (#27) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain C (#22), sequence alignment score =
147.7
RMSD between 34 pruned atom pairs is 0.492 angstroms; (across all 36 pairs:
1.239)
> save /Users/alexandrakaragiaridi/Desktop/image1.png supersample 3
> cartoon style #22,27 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image2.png supersample 3
> cartoon style #22,27 xsection oval modeHelix default
> moprh #22,27 frames 60
Unknown command: moprh #22,27 frames 60
> morph #22,27 frames 60
Computed 61 frame morph #31
> coordset #31 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!31 models
> show #!27 models
> show #!22 models
> morph #27,22 frames 60
Computed 61 frame morph #32
> coordset #32 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!32 models
> show #!27 models
> show #!22 models
> matchmaker #22/b:52-87 to #27/b:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_nuc_MolA_deleted.pdb, chain B (#27) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain B (#22), sequence alignment score =
163.5
RMSD between 32 pruned atom pairs is 0.522 angstroms; (across all 33 pairs:
0.675)
> save /Users/alexandrakaragiaridi/Desktop/image3.png supersample 3
> cartoon style #22,27 modeHelix tube sides 20
> save /Users/alexandrakaragiaridi/Desktop/image4.png supersample 3
> cartoon style #22,27 xsection oval modeHelix default
> morph #27,22 frames 60
Computed 61 frame morph #33
> coordset #33 1,61
> hide #!33 atoms
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!33 models
> show #!27 models
> show #!22 models
> morph #22,27 frames 60
Computed 61 frame morph #34
> coordset #34 1,61
> movie record
> movie encode /Users/alexandrakaragiaridi/Desktop/movie.mp4 framerate 25.0
Movie saved to /Users/alexandrakaragiaridi/Desktop/movie.mp4
> hide #!34 models
> show #!22 models
> show #!10 models
> matchmaker #22/c:52-87 to #10/c:52-87
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain C (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain C (#22), sequence alignment score =
144.1
RMSD between 34 pruned atom pairs is 0.463 angstroms; (across all 36 pairs:
1.176)
> view
> matchmaker #22/c:52-87 to #10/c:52-87 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain C (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain C (#22), sequence alignment score =
144.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: MolABC_no_nuc_MolA_deleted.pdb
#10/C, MolBC_WT_in_DDM_chains_renamed.pdb #22/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 34 pruned atom pairs is 0.463 angstroms; (across all 36 pairs:
1.176)
> ui tool show "Render By Attribute"
> matchmaker #22 to #10 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MolABC_no_nuc_MolA_deleted.pdb, chain B (#10) with
MolBC_WT_in_DDM_chains_renamed.pdb, chain B (#22), sequence alignment score =
1433.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: MolABC_no_nuc_MolA_deleted.pdb
#10/B, MolBC_WT_in_DDM_chains_renamed.pdb #22/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 292 pruned atom pairs is 0.573 angstroms; (across all 301 pairs:
0.895)
> ui tool show "Render By Attribute"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 759, in _set_value_cb
self._redraw_cb()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb
self._bins = left + filled_bins + right
ValueError: operands could not be broadcast together with shapes (0,) (64,)
ValueError: operands could not be broadcast together with shapes (0,) (64,)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb
self._bins = left + filled_bins + right
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 760, in _set_value_cb
self._move_cur_marker(v)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 570, in _move_cur_marker
self._active_markers._update_plot()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 1222, in _update_plot
self._update_marker_coordinates()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 1207, in
_update_marker_coordinates
x, y = self._scene_xy(m.xy)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 1090, in _scene_xy
return self.histogram._scene_xy(abs_xy)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 179, in <lambda>
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 714, in _select_marker_cb
self._set_sel_marker(marker, drag_start=event)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 743, in _set_sel_marker
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 180, in <lambda>
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 576, in _move_marker_cb
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
TypeError: object of type 'function' has no len()
TypeError: object of type 'function' has no len()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/histogram.py", line 441, in _abs_xy
num_bins = len(self._bins)
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6.3 (21G419)
Kernel Version: Darwin 21.6.0
Time since boot: 19:06
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
SB220Q:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: c7.76
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
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: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
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-Clipper: 0.21.0
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: 1.6.1
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-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: 2.7.2
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: 1.10.3
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: 1.6.7
decorator: 5.1.1
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: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
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
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: 21.3
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: 3.5.0
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
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
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: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
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
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