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#17360 closed defect (duplicate)
MOLE JSON: atom radius must be positive
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
[deleted to fit within ticket limits]
> 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
Change History (5)
comment:1 by , 7 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MOLE JSON: atom radius must be positive |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
comment:3 by , 7 months ago
I don't see how this ticket is related to MOLE json radius 0. The tracebacks are all from render by attribute, somehow self._bins being a function.
comment:4 by , 7 months ago
Yeah, the error actually being reported is a histogram-widget problem that has been fixed for awhile. The JSON-related error is in the part of the description that was deleted for length, namely:
open
8156 > /Users/alexandrakaragiaridi/Desktop/Pore_for_MolABC_E154Q_AMPPNP_in_DDM.json
8157
8158 Traceback (most recent call last):
8159 File
8160 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8161 packages/chimerax/open_command/dialog.py", line 162, in _qt_safe
8162 run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
8163 File
8164 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8165 packages/chimerax/core/commands/run.py", line 38, in run
8166 results = command.run(text, log=log, return_json=return_json)
8167 File
8168 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8169 packages/chimerax/core/commands/cli.py", line 2897, in run
8170 result = ci.function(session, kw_args)
8171 File
8172 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8173 packages/chimerax/open_command/cmd.py", line 119, in cmd_open
8174 models = Command(session, registry=registry).run(provider_cmd_text,
8175 log=log)[0]
8176 File
8177 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8178 packages/chimerax/core/commands/cli.py", line 2897, in run
8179 result = ci.function(session, kw_args)
8180 File
8181 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8182 packages/chimerax/open_command/cmd.py", line 194, in provider_open
8183 models, status = collated_open(session, None, [data], data_format,
8184 _add_models,
8185 File
8186 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8187 packages/chimerax/open_command/cmd.py", line 464, in collated_open
8188 return remember_data_format()
8189 File
8190 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8191 packages/chimerax/open_command/cmd.py", line 435, in remember_data_format
8192 models, status = func(*func_args, func_kw)
8193 File
8194 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8195 packages/chimerax/mole/init.py", line 27, in open
8196 return mole.read_mole_json(session, data, file_name, kw)
8197 File
8198 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8199 packages/chimerax/mole/mole.py", line 44, in read_mole_json
8200 models = channel_models(session, jChannels, transparency/100.0)
8201 File
8202 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8203 packages/chimerax/mole/mole.py", line 83, in channel_models
8204 ms.create_marker((x,y,z), color, r)
8205 File
8206 "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
8207 packages/chimerax/markers/markers.py", line 26, in create_marker
8208 a.radius = radius
8209 File "atomic_cpp/cymol.pyx", line 456, in
8210 chimerax.atomic.cymol.CyAtom.radius.set
8211 RuntimeError: radius must be positive
8212
8213 RuntimeError: radius must be positive
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Duplicate of #9745