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Opened 8 months ago
Last modified 8 months ago
#17114 assigned defect
ChimeraX forgets matchmaker command after installing other bundles
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/ruidi/Desktop/065_ntsr1/analysis_results/crystalanalysis/0227/0304.cxs
> format session
Log from Tue Mar 4 14:50:56 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2 C1 model
> J4765_arrestin2-coot-1.pdb"
> "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N065 model
> -coot-9-2.pdb" "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N191
> model _R-lig-coot-4.pdb"
Chain information for NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb #1
---
Chain | Description
B | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
Chain information for NTSR1-ARRB2-N065 model -coot-9-2.pdb #2
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
Chain information for NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb #3
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
> hide surfaces
> hide cartoons
> show cartoons
> style stick
Changed 34157 atom styles
> hide atoms
> set bgColor white
> ui tool show Matchmaker
> matchmaker #!1 to #3/E pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain E (#3) with
NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain B (#1), sequence
alignment score = 1584.4
RMSD between 288 pruned atom pairs is 0.813 angstroms; (across all 322 pairs:
1.447)
> ui tool show Matchmaker
> matchmaker #!1 to #3/E pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain E (#3) with
NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain B (#1), sequence
alignment score = 1584.4
RMSD between 288 pruned atom pairs is 0.813 angstroms; (across all 322 pairs:
1.447)
> matchmaker #!1 to #2/A pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain E (#1), sequence alignment score =
1702.4
RMSD between 334 pruned atom pairs is 0.628 angstroms; (across all 344 pairs:
0.803)
> matchmaker #!1 to #2/D pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain D (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain D (#1), sequence alignment score =
1058.1
RMSD between 214 pruned atom pairs is 0.669 angstroms; (across all 221 pairs:
0.794)
> matchmaker #!1 to #2/L pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain L (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain L (#1), sequence alignment score =
29.6
RMSD between 6 pruned atom pairs is 0.727 angstroms; (across all 6 pairs:
0.727)
> matchmaker #!1 to #3/A pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain A (#3) with
NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain E (#1), sequence
alignment score = 1734.8
RMSD between 338 pruned atom pairs is 0.673 angstroms; (across all 344 pairs:
0.773)
> matchmaker #!1 to #3/D pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain D (#3) with
NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain D (#1), sequence
alignment score = 1078.5
RMSD between 208 pruned atom pairs is 0.687 angstroms; (across all 221 pairs:
0.918)
> matchmaker #!1 to #3/E pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain E (#3) with
NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain B (#1), sequence
alignment score = 1584.4
RMSD between 288 pruned atom pairs is 0.813 angstroms; (across all 322 pairs:
1.447)
> matchmaker #!1 to #3/L pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain L (#3) with
NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain L (#1), sequence
alignment score = 29.6
RMSD between 6 pruned atom pairs is 0.739 angstroms; (across all 6 pairs:
0.739)
> matchmaker #!1 to #3/L pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain L (#3) with
NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain L (#1), sequence
alignment score = 29.6
RMSD between 6 pruned atom pairs is 0.739 angstroms; (across all 6 pairs:
0.739)
> matchmaker #!1 to #2/E pairing bs
Parameters
---
Chain pairing | bs
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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain E (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain B (#1), sequence alignment score =
1561.6
RMSD between 280 pruned atom pairs is 0.760 angstroms; (across all 322 pairs:
1.539)
> matchmaker #!2-3 to #1
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 NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain E (#1) with
NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2), sequence alignment score =
1702.4
RMSD between 334 pruned atom pairs is 0.628 angstroms; (across all 344 pairs:
0.803)
Matchmaker NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain E (#1) with
NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain A (#3), sequence alignment
score = 1734.8
RMSD between 338 pruned atom pairs is 0.673 angstroms; (across all 344 pairs:
0.773)
> matchmaker #!3 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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2) with
NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain A (#3), sequence alignment
score = 1720.4
RMSD between 335 pruned atom pairs is 0.359 angstroms; (across all 344 pairs:
0.550)
> 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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain E (#1), sequence alignment score =
1702.4
RMSD between 334 pruned atom pairs is 0.628 angstroms; (across all 344 pairs:
0.803)
> matchmaker #!2-3 to #1
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 NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain E (#1) with
NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2), sequence alignment score =
1702.4
RMSD between 334 pruned atom pairs is 0.628 angstroms; (across all 344 pairs:
0.803)
Matchmaker NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain E (#1) with
NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain A (#3), sequence alignment
score = 1734.8
RMSD between 338 pruned atom pairs is 0.673 angstroms; (across all 344 pairs:
0.773)
> matchmaker #!2-3 to #1
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 NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain E (#1) with
NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2), sequence alignment score =
1702.4
RMSD between 334 pruned atom pairs is 0.628 angstroms; (across all 344 pairs:
0.803)
Matchmaker NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, chain E (#1) with
NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain A (#3), sequence alignment
score = 1734.8
RMSD between 338 pruned atom pairs is 0.673 angstroms; (across all 344 pairs:
0.773)
> matchmaker #3/E to #2/E & sel pairing ss
No 'to' chains specified
> matchmaker #2/E to #1/D & sel pairing ss
No 'to' chains specified
> matchmaker #!1 to #2/E & sel pairing bs
No 'to' chains specified
> ui tool show Matchmaker
> ui tool show "Show Sequence Viewer"
> select add #1/D:29
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #1/D:30
26 atoms, 24 bonds, 2 residues, 1 model selected
> select #1/L#2/L#3/L
240 atoms, 243 bonds, 18 residues, 3 models selected
> select #1/D#2/D#3/D
6591 atoms, 6720 bonds, 663 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> select #1/Q#2/Q#3/Q
6071 atoms, 6173 bonds, 648 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> select #1:.E
Expected an objects specifier or a keyword
> select #1:.E
Expected an objects specifier or a keyword
> select #1:E
Nothing selected
> select #1/E
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> setattr residues chainID X sel
Expected a keyword
> setattr chain chainID X sel
Expected a keyword
> changechains chain chainID X sel
Expected ',' or a keyword
> changechains #1/A X
No residues specified
> changechains #1:.A X
No residues specified have any of the 'from' chain IDs
> list models
Unknown command: list models
> models list
Unknown command: models list
> info
6 models
#1, NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb, shown
10706 atoms, 10836 bonds, 674 residues, 3 chains (B,C,E,L,R)
2 missing structure
#1.1, missing structure, shown, 2 pseudobonds
#2, NTSR1-ARRB2-N065 model -coot-9-2.pdb, shown
5416 atoms, 5550 bonds, 674 residues, 3 chains (A,C,E,L,R)
2 missing structure
#2.1, missing structure, shown, 2 pseudobonds
#3, NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, shown
5373 atoms, 5507 bonds, 673 residues, 3 chains (A,E,L)
2 missing structure
#3.1, missing structure, shown, 2 pseudobonds
> changechains #1:.E X
No residues specified have any of the 'from' chain IDs
> changechains #1/E X
Chain IDs of 344 residues changed
> changechains #2/A X
Chain IDs of 344 residues changed
> changechains #3/A X
Chain IDs of 344 residues changed
> changechains #2/E A
Chain IDs of 322 residues changed
> changechains #3/E A
Chain IDs of 323 residues changed
> changechains #1/B A
Chain IDs of 322 residues changed
> changechains #X B
No residues specified have any of the 'from' chain IDs
> changechains #1/X B
Chain IDs of 344 residues changed
> changechains #2/X B
Chain IDs of 344 residues changed
> changechains #3/X B
Chain IDs of 344 residues changed
> matchmaker #1/A to #0/A
No 'to' model specified
> matchmaker #1/A to #2/A
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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain A (#1), sequence alignment score =
1561.6
RMSD between 280 pruned atom pairs is 0.760 angstroms; (across all 322 pairs:
1.539)
> matchmaker #3/A to #2/A
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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain A (#2) with
NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain A (#3), sequence alignment
score = 1637.8
RMSD between 302 pruned atom pairs is 0.713 angstroms; (across all 322 pairs:
1.077)
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> listinfo chain
chain id #1/A chain_id A
chain id #1/B chain_id B
chain id #1/L chain_id L
chain id #2/B chain_id B
chain id #2/A chain_id A
chain id #2/L chain_id L
chain id #3/B chain_id B
chain id #3/A chain_id A
chain id #3/L chain_id L
> sort
Unknown command: sort
> select #2/A#3/A
5119 atoms, 5253 bonds, 4 pseudobonds, 645 residues, 4 models selected
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> select #1/E#2/E#3/E
Nothing selected
> select #1/E#2/E#3/E
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/L #2/L #3/L
Alignment identifier is 1
> sequence chain #1/A #2/A #3/A
Alignment identifier is 2
> sequence chain #1/B #2/B #3/B
Alignment identifier is 3
> select ::name="LIG"
69 atoms, 77 bonds, 2 residues, 2 models selected
> style sel stick
Changed 69 atom styles
> show sel atoms
> select ::name="SRW"
33 atoms, 37 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> select #1
10706 atoms, 10836 bonds, 2 pseudobonds, 674 residues, 2 models selected
> ui tool show "Model Panel"
> rename #1 NTSR1-ARRB2-SBI553.pdb
> rename #2 NTSR1-ARRB2-N065.pdb
> rename #3 NTSR1-ARRB2-N191.pdb
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #d6ffffff
> color (#!1 & sel) #d6e6ffff
> color (#!1 & sel) #d6e6d5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d3e6d5ff
> color (#!1 & sel) #d2e6d5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d0e6d5ff
> color (#!1 & sel) #cfe6d5ff
> color (#!1 & sel) #cce6d5ff
> color (#!1 & sel) #cbe6d5ff
> color (#!1 & sel) #cae6d5ff
> color (#!1 & sel) #c8e6d5ff
> color (#!1 & sel) #c7e6d5ff
> color (#!1 & sel) #c6e6d5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #c5e6d5ff
> color (#!1 & sel) #c4e6d5ff
> color (#!1 & sel) #c3e6d5ff
> color (#!1 & sel) #c2e6d5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #bfe6d5ff
> color (#!1 & sel) #bde6d5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #31e6d5ff
> color (#!1 & sel) #d6e6d5ff
> color (#!1 & sel) #c4e6d5ff
> color (#!1 & sel) #b5e6d5ff
[Repeated 1 time(s)]
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel #31e6d5ff
> color sel #31cad5ff
> color sel #31cad0ff
> color sel byelement
[Repeated 2 time(s)]
> color sel #f1eeedff
> color sel #f0eeedff
> color sel #e5eeedff
> color sel #d6eeedff
> color sel #d5eeedff
> color sel #c5eeedff
> color sel #c2eeedff
> color sel #beeeedff
> color sel #bdeeedff
> color sel #baeeedff
> color sel #b4eeedff
> color sel #b3eeedff
> color sel #b0eeedff
> color sel #afeeedff
> color sel #a6eeedff
[Repeated 1 time(s)]
> color sel #a4eeedff
[Repeated 3 time(s)]
> color sel #a6eeedff
[Repeated 1 time(s)]
> color sel #a7eeedff
> color sel #aaeeedff
> color sel #aceeedff
> color sel #adeeedff
> color sel #aeeeedff
> color sel #afeeedff
> color sel #b0eeedff
> color sel #b1eeedff
> color sel #b2eeedff
> color sel #b3eeedff
[Repeated 1 time(s)]
> color sel #b4eeedff
[Repeated 1 time(s)]
> color sel #b5eeedff
> color sel #b6eeedff
> color sel #b7eeedff
> color sel #b8eeedff
> color sel #baeeedff
[Repeated 1 time(s)]
> color sel #bbeeedff
> color sel #bceeedff
> color sel #beeeedff
[Repeated 1 time(s)]
> color sel #beefedff
> color sel #bef0edff
> color sel #bef1edff
> color sel #bef2edff
[Repeated 2 time(s)]
> color sel #bef3edff
> color sel #bef4edff
> color sel #bef5edff
[Repeated 2 time(s)]
> color sel #bef5e8ff
> color sel #bef5e4ff
> color sel #bef5e1ff
> color sel #bef5dcff
> color sel #bef5d8ff
> color sel #bef5d6ff
[Repeated 1 time(s)]
> color sel #bef5d5ff
> color sel #bef5d4ff
[Repeated 1 time(s)]
> color sel #bef5d3ff
> color sel #bef5d2ff
[Repeated 1 time(s)]
> color sel #bef5d1ff
> color sel #bef5d0ff
> color sel #bef5cfff
> color sel #bef5ceff
> color sel #bef5cdff
> color sel #bef5ccff
> color sel #bef5cbff
> color sel #bef5caff
> color sel #bef5c9ff
> color sel #bef5c8ff
> color sel #bef5c7ff
> color sel #bef5c6ff
> color sel #bef5c4ff
[Repeated 1 time(s)]
> color sel #bef5c2ff
> color sel #bef5c1ff
> color sel #bef5c0ff
[Repeated 1 time(s)]
> color sel #bef5bfff
> color sel #bef5bdff
> color sel #bef5bcff
> color sel #bef5bbff
> color sel #bef5baff
> color sel #bef5b8ff
> color sel #bef5b6ff
[Repeated 1 time(s)]
> color sel #bef5b5ff
> color sel #bef5b4ff
> color sel #bef5b3ff
> color sel #bef5b2ff
[Repeated 2 time(s)]
> color sel #bef5b1ff
> color sel #bef5b0ff
[Repeated 1 time(s)]
> color sel #bef5afff
> color sel #bef5b0ff
> color sel #bef5b4ff
> color sel #bef5b7ff
> color sel #bef5c3ff
> color sel #bef5cbff
> color sel #bef5cdff
> color sel #bef5cfff
> color sel #bdf5cfff
> color sel #bbf5cfff
> color sel #b7f5cfff
> color sel #b2f5cfff
> color sel #a9f5cfff
> color sel #a8f5cfff
> color sel #a3f5cfff
> color sel #a0f5cfff
> color sel #9ff5cfff
[Repeated 1 time(s)]
> color sel #9ef5cfff
> color sel #9bf5cfff
> color sel #9af5cfff
> color sel #99f5cfff
[Repeated 3 time(s)]
> color sel #31f5cfff
[Repeated 1 time(s)]
> color sel #31cacfff
> color sel #31cad0ff
> color sel #91b6a8ff
> color sel #cffff1ff
[Repeated 2 time(s)]
> color sel #cfe6f1ff
> color sel #d6e6f1ff
> color sel #d6e6d5ff
> color sel byelement
> color sel byhetero
> color sel byelement
> color sel bychain
> color sel bynucleotide
> color sel bychain
> color sel bynucleotide
> color sel bychain
> color sel bypolymer
> color sel bynucleotide
> color sel bychain
> color sel #c1fbc0ff
> color sel #38ff2cff
> color sel bychain
> color sel #38ff2cff
[Repeated 1 time(s)]
> color sel #31ff2cff
> color sel #31ca2cff
> color sel #31ca41ff
> color sel #31ca52ff
> color sel #31ca66ff
> color sel #31cab5ff
> color sel #31cadcff
> color sel #31cad1ff
> color sel #31cabcff
> color sel #31ca95ff
> color sel #31ca94ff
[Repeated 1 time(s)]
> color sel #31df94ff
> color sel #31bc94ff
> color sel #31af94ff
> color sel #31bc94ff
> color sel #31ac94ff
[Repeated 1 time(s)]
> color sel #31aa94ff
> color sel #31aa7eff
> color sel #31aa6eff
[Repeated 1 time(s)]
> color sel #31aae6ff
> color sel #31d6e6ff
> color sel #31b8e6ff
> color sel #319de6ff
> color sel #31b6e6ff
No target buttons for the coloring action are checked
> select #1/C elem N
Expected a keyword
> select #1/C@N
Nothing selected
> listinfo atoms #1/C
atom id #1/C:503@C1 idatm_type C3
atom id #1/C:503@N1 idatm_type N3
atom id #1/C:503@O1 idatm_type O3
atom id #1/C:503@C2 idatm_type Car
atom id #1/C:503@N2 idatm_type N2
atom id #1/C:503@O2 idatm_type O2
atom id #1/C:503@C3 idatm_type Car
atom id #1/C:503@N3 idatm_type N2
atom id #1/C:503@C4 idatm_type Car
atom id #1/C:503@N4 idatm_type Npl
atom id #1/C:503@C5 idatm_type Car
atom id #1/C:503@C6 idatm_type Car
atom id #1/C:503@C7 idatm_type Car
atom id #1/C:503@C8 idatm_type C3
atom id #1/C:503@C9 idatm_type C3
atom id #1/C:503@C10 idatm_type C3
atom id #1/C:503@C11 idatm_type C3
atom id #1/C:503@C12 idatm_type C3
atom id #1/C:503@C13 idatm_type Car
atom id #1/C:503@C14 idatm_type Car
atom id #1/C:503@C15 idatm_type Car
atom id #1/C:503@C16 idatm_type Car
atom id #1/C:503@C17 idatm_type Car
atom id #1/C:503@C18 idatm_type Car
atom id #1/C:503@C19 idatm_type Car
atom id #1/C:503@C20 idatm_type Car
atom id #1/C:503@C21 idatm_type C3
atom id #1/C:503@C22 idatm_type C3
atom id #1/C:503@C23 idatm_type C2
atom id #1/C:503@C24 idatm_type C3
atom id #1/C:503@C25 idatm_type C3
atom id #1/C:503@C26 idatm_type C3
atom id #1/C:503@F1 idatm_type F
> select #1/C @N
Nothing selected
> select #1/C@N
Nothing selected
> select #1:/.C@N
Expected an objects specifier or a keyword
> select element N and #1/C
Expected an objects specifier or a keyword
> select element N and #1/C
Expected an objects specifier or a keyword
> select #1/C@.N
Expected an objects specifier or a keyword
> select #1/C and @N
Expected a keyword
> select #1 & :C & @N
Nothing selected
> select #1/C/N
33 atoms, 37 bonds, 1 residue, 1 model selected
> select #1/C/@N
Expected an objects specifier or a keyword
> select #1/C/elem N
Expected a keyword
> select #1/C/.N
Expected an objects specifier or a keyword
> select #1:.C@N
Expected an objects specifier or a keyword
> color sel byhetero
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel #f5b582ff target a
[Repeated 2 time(s)]
> color sel #efb582ff target a
[Repeated 1 time(s)]
> color sel #efaf82ff target a
> color sel byhetero
> select #3/C
Nothing selected
> changechains #3/A.LIG C
No residues specified have any of the 'from' chain IDs
> changechains #3/A/LIG C
Chain IDs of 323 residues changed
> select #3/C
2576 atoms, 2645 bonds, 2 pseudobonds, 323 residues, 2 models selected
> select #3/C
2576 atoms, 2645 bonds, 2 pseudobonds, 323 residues, 2 models selected
> changechains #3/C A
Chain IDs of 323 residues changed
> changechains #3:A.LIG C
No residues specified have any of the 'from' chain IDs
> changechains #3:A:LIG C
Chain IDs of 1 residues changed
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel #bfd3b5ff target a
> color sel #bfdfb5ff target a
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> color sel #bfdfb5ff target a
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency 50,r
Missing or invalid "percent" argument: Expected a number
> transparency 50
> transparency 50 models #1
Expected ',' or a keyword
> transparency 50 models #1
Expected ',' or a keyword
> transparency #1 50 All
> set silhouettes true
> set silhouetteWidth 3
> set silhouetteColor black
> select #3/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> color (#!3 & sel) #bfdfb5ff target a
> color (#!3 & sel) #a5dfb5ff target a
[Repeated 1 time(s)]
> color (#!3 & sel) #a5d2b5ff target a
> color (#!3 & sel) #a5d2e6ff target a
> color (#!3 & sel) #99d2e6ff target a
> color (#!3 & sel) #a6d2e6ff target a
[Repeated 1 time(s)]
> color (#!3 & sel) #a5d2e6ff target a
> color (#!3 & sel) #e8faffff target a
> color (#!3 & sel) #a5faffff target a
> color (#!3 & sel) #a5d2ffff target a
> color (#!3 & sel) #a5d2e6ff target a
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> color (#!1 & sel) #a5d3e6ff target a
> color (#!1 & sel) #c0e6a5ff target a
> color (#!1 & sel) #c0e6a6ff target a
> color (#!1 & sel) #81e63aff target a
> color (#!1 & sel) #81e639ff target a
> color (#!1 & sel) #70c732ff target a
[Repeated 1 time(s)]
> color (#!1 & sel) #00c732ff target a
> color (#!1 & sel) #f2c732ff target a
[Repeated 1 time(s)]
> color (#!1 & sel) #f2bf32ff target a
[Repeated 1 time(s)]
> color (#!1 & sel) #f2bfc7ff target a
> color (#!1 & sel) #f2bfd8ff target a
> color (#!1 & sel) #f2bfc7ff target a
> select #2A
Expected an objects specifier or a keyword
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!2 & sel) #f2bfc6ff
> color (#!2 & sel) #f2bfc7ff
> select #3/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> color (#!3 & sel) #a5bfc7ff
> color (#!3 & sel) #a5d2c7ff
> color (#!3 & sel) #a5d2e6ff
> transparency #2 50 All
> transparency #3 50 All
> set silhouettes true
> set silhouetteWidth 3
> set silhouetteColor black
> transparency #3 50 All
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> set silhouettes true
> set silhouetteWidth 3
> set silhouetteColor black
> select A
Expected an objects specifier or a keyword
> open /Users/ruidi/Desktop/咩～/gromacs_no_water2.gro
Chain information for GROningen MAchine for Chemical Simulation #4
---
Chain | Description
? | No description available
> open /Users/ruidi/Desktop/咩～/conver.py
executed conver.py
> open /Users/ruidi/Desktop/咩～/gromacs_no_water.gro
Chain information for GROningen MAchine for Chemical Simulation #5
---
Chain | Description
? | No description available
> open /Users/ruidi/Desktop/咩～/gromacs_no_water2.gro
Chain information for GROningen MAchine for Chemical Simulation #6
---
Chain | Description
? | No description available
> open /Users/ruidi/Desktop/咩～/conver.py
executed conver.py
> open /Users/ruidi/Desktop/咩～/gromacs_no_water.gro
Chain information for GROningen MAchine for Chemical Simulation #7
---
Chain | Description
? | No description available
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel #00ede9ff
> color sel #00d5e9ff
> color sel #31d5e9ff
[Repeated 1 time(s)]
> color sel #31cae9ff
> color sel #31cad0ff
> listinfo models
model id #1 type AtomicStructure name NTSR1-ARRB2-SBI553.pdb
model id #1.1 type PseudobondGroup name "missing structure"
model id #2 type AtomicStructure name NTSR1-ARRB2-N065.pdb
model id #2.1 type PseudobondGroup name "missing structure"
model id #3 type AtomicStructure name NTSR1-ARRB2-N191.pdb
model id #3.1 type PseudobondGroup name "missing structure"
model id #4 type AtomicStructure name "GROningen MAchine for Chemical
Simulation"
model id #5 type AtomicStructure name "GROningen MAchine for Chemical
Simulation"
model id #6 type AtomicStructure name "GROningen MAchine for Chemical
Simulation"
model id #7 type AtomicStructure name "GROningen MAchine for Chemical
Simulation"
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> color sel #efaf82ff
> color sel byhetero
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> select #2/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> color sel #39e8efff
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel #bad4b2ff
> color sel #96b27eff
> color sel byhetero
> select #3/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> select #3/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> color sel #e6838aff
> color sel #96b27eff
> select #3
5373 atoms, 5507 bonds, 2 pseudobonds, 673 residues, 2 models selected
> select #4
6173 atoms, 6243 bonds, 395 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5
6315 atoms, 6384 bonds, 398 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6
6173 atoms, 6243 bonds, 395 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> delete atoms
> delete bonds
> open /Users/ruidi/Desktop/咩～/conver.py format python
No such file/path: /Users/ruidi/Desktop/咩～/conver.py
> open /Users/ruidi/Desktop/咩～/conver.py format python
No such file/path: /Users/ruidi/Desktop/咩～/conver.py
> open /Users/ruidi/Desktop/咩～/gromacs_no_water.gro format gro
No such file/path: /Users/ruidi/Desktop/咩～/gromacs_no_water.gro
> open /Users/ruidi/Desktop/咩～/gromacs_no_water2.gro format gro
No such file/path: /Users/ruidi/Desktop/咩～/gromacs_no_water2.gro
> open /Users/ruidi/Desktop/咩～/conver.py format python
No such file/path: /Users/ruidi/Desktop/咩～/conver.py
> open /Users/ruidi/Desktop/咩～/gromacs_no_water2.gro format gro
No such file/path: /Users/ruidi/Desktop/咩～/gromacs_no_water2.gro
> open /Users/ruidi/Desktop/111.mol2 format mol2
Chain information for fold_2025_01_09_16_07_model_0.cif #1.1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for fold_2025_01_09_16_07_model_1.cif #1.2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for fold_2025_01_09_16_07_model_2.cif #1.3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for fold_2025_01_09_16_07_model_3.cif #1.4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Chain information for fold_2025_01_09_16_07_model_4.cif #1.5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Opened 111.mol2 containing 5 structures (41635 atoms, 42475 bonds)
> viewdockx #1.1-5
No suitable models found for ViewDockX
> select all\
Expected an objects specifier or a keyword
> select
41635 atoms, 42475 bonds, 5310 residues, 6 models selected
> delete atoms sel
> delete bonds sel
> listinfo model
model id #1 type Model name 111.mol2
> close session
> open "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2 C1 model
> J4765_arrestin2-coot-1.pdb"
> "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N065 model
> -coot-9-2.pdb" "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N191
> model _R-lig-coot-4.pdb"
Chain information for NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb #1
---
Chain | Description
B | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
Chain information for NTSR1-ARRB2-N065 model -coot-9-2.pdb #2
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
Chain information for NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb #3
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
> hide surfaces
[Repeated 1 time(s)]
> show atoms
> show cartoons
> style sphere
Changed 34157 atom styles
> style sphere
Changed 34157 atom styles
> volume hide
No volumes specified
> hide atoms
> select #1/D
3277 atoms, 3320 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/Q
2975 atoms, 3009 bonds, 216 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/Q
1548 atoms, 1582 bonds, 216 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/D
1657 atoms, 1700 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #/D
Expected an objects specifier or a keyword
> select #3/D
1657 atoms, 1700 bonds, 221 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/Q
1548 atoms, 1582 bonds, 216 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> matchmaker #1/B to #2/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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain E (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain B (#1), sequence alignment score =
1561.6
RMSD between 280 pruned atom pairs is 0.760 angstroms; (across all 322 pairs:
1.539)
> matchmaker #3/E to #2/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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain E (#2) with
NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain E (#3), sequence alignment
score = 1637.8
RMSD between 302 pruned atom pairs is 0.713 angstroms; (across all 322 pairs:
1.077)
> select ::name="LIG"
69 atoms, 77 bonds, 2 residues, 2 models selected
> show sel target ab
> show sel atoms
> hide sel surfaces
> style sel sphere
Changed 69 atom styles
> hide sel cartoons
> show sel cartoons
[Repeated 1 time(s)]
> hide sel surfaces
> hide sel atoms
> show sel atoms
> hide sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
[Repeated 1 time(s)]
> color sel byhetero
> color sel bychain
> rainbow sel
> style sel sphere
Changed 69 atom styles
> surface hidePatches sel
> show sel target ab
> style sel stick
Changed 69 atom styles
> select ::name="SRW"
33 atoms, 37 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 33 atom styles
> ui tool show "Color Actions"
> changechains #3/E/LIG C
Chain IDs of 323 residues changed
> color sel #19b8b7ff
> color sel byhetero
[Repeated 1 time(s)]
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> color sel #f5b482ff
> color sel #efaf82ff
> color sel byhetero
> select #3/C
2576 atoms, 2645 bonds, 2 pseudobonds, 323 residues, 2 models selected
> select #3/C
2576 atoms, 2645 bonds, 2 pseudobonds, 323 residues, 2 models selected
> undo
[Repeated 2 time(s)]
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> select #2/A
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> changechains #2/A X
Chain IDs of 344 residues changed
> changechains #3/A X
Chain IDs of 344 residues changed
> changechains #1/E X
Chain IDs of 344 residues changed
> changechains #1/B A
Chain IDs of 322 residues changed
> changechains #3/C A
Chain IDs of 323 residues changed
> changechains #2/E A
Chain IDs of 322 residues changed
> changechains #2/X B
Chain IDs of 344 residues changed
> changechains #3/X B
Chain IDs of 344 residues changed
> changechains #1/X B
Chain IDs of 344 residues changed
> color sel #d37538ff
> color sel #828c9eff
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> color sel #f5b482ff
> color sel #efaf82ff
> color sel #d37538ff
[Repeated 1 time(s)]
> color sel #d37638ff
> color sel #d37738ff
[Repeated 1 time(s)]
> color sel #d37838ff
> color sel #d37938ff
> color sel #d37c38ff
> color sel #d37d38ff
> color sel #d37e38ff
[Repeated 1 time(s)]
> color sel #d38038ff
[Repeated 1 time(s)]
> color sel #d38138ff
> color sel #d38238ff
> color sel #d38338ff
> color sel #d38438ff
[Repeated 1 time(s)]
> color sel #d38538ff
[Repeated 1 time(s)]
> color sel #d38738ff
> color sel #d38938ff
> color sel #d38a38ff
> color sel #d38c38ff
> color sel #d38c44ff
[Repeated 1 time(s)]
> color sel #d38c45ff
[Repeated 1 time(s)]
> color sel #d38c46ff
[Repeated 1 time(s)]
> color sel #d38c47ff
[Repeated 1 time(s)]
> color sel #d48c47ff
> color sel #d58c47ff
[Repeated 2 time(s)]
> color sel #d68c47ff
[Repeated 1 time(s)]
> color sel #da8c47ff
> color sel #db8c47ff
[Repeated 1 time(s)]
> color sel #dc8c47ff
> color sel #dc8c38ff
[Repeated 1 time(s)]
> color sel #d38c38ff
[Repeated 1 time(s)]
> color sel #d37538ff
> color sel #ef7538ff
> color sel #efaf38ff
> color sel #efaf82ff
> color sel byhetero
> select #3/C
Nothing selected
> changechains #3/A/LIG C
Chain IDs of 323 residues changed
> select #3/C
2576 atoms, 2645 bonds, 2 pseudobonds, 323 residues, 2 models selected
> changechains #3/C A
Chain IDs of 323 residues changed
> changechains #3:A:LIG C
Chain IDs of 1 residues changed
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel #96b27eff
> color sel byhetero
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> Model Panel
Unknown command: Model Panel
> ui tool show "Model Panel"
> rename #1 NTSR1-ARRB2-SBI553.pdb
> rename #2 NTSR1-ARRB2-N065.pdb
> rename #3 NTSR1-ARRB2-N191.pdb
> hide #!3 models
> hide #!2 models
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> color (#!1 & sel) #a5b27eff
> color (#!1 & sel) #a5d27eff
> color (#!1 & sel) #a5d2e6ff
> transparency #1 50 All
> set silhouettes true
> set silhouetteWidth 3
> set silhouetteColor black
> set silhouettes false
> set silhouetteWidth 1
> set silhouetteColor none
Invalid "silhouetteColor" argument: Invalid color name or specifier
> set silhouetteColor none
Invalid "silhouetteColor" argument: Invalid color name or specifier
> transparency #1 50 All
> transparency #1 80 All
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency #1/C 0
> transparency #1 0 All
> transparency #1/A 80 All
> transparency #1/A 60 All
> transparency #1/B 60 All
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> set silhouettes true
> set silhouetteWidth 3
[Repeated 1 time(s)]
> set silhouetteColor black
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> set silhouettes false sel
Expected keyword "selectionColor" or "selectionWidth"
> set silhouetteColor none sel
Invalid "silhouetteColor" argument: Invalid color name or specifier
> set silhouetteWidth 1 sel
Expected keyword "selectionColor" or "selectionWidth"
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> set silhouettes false sel
Expected keyword "selectionColor" or "selectionWidth"
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> color sel #1bcdccff
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> set silhouettes false
> transparency #1 50 All
> transparency #1/C 0 All
> transparency #1/L 0 All
> transparency #1 80 All
> transparency #1/L 0 All
> transparency #1/C 0 All
> select #1/A and #1/B
Expected a keyword
> select #1/A and #1/B
Expected a keyword
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> stick sel
Unknown command: stick sel
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> set silhouettes true
> set silhouettes false
> set silhouettes true #1/A
Expected a keyword
> show silhouette
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> set silhouettes true
> set silhouettes false
> set silhouettes true target c
Expected a keyword
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> select #1/A set silhouettes true
Expected a keyword
> set silhouettes true sele
Expected keyword "selectionColor" or "selectionWidth"
> set silhouettes true sel
Expected keyword "selectionColor" or "selectionWidth"
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> set silhouettes true selectionColor gray selectionWidth 2
> toolshed show
> set silhouettes false
> show silhouettes :#1/A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show silhouettes @#1/A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show silhouettes #1/A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> set silhouettes true #1/A
Expected a keyword
> set silhouettes true #1/B
Expected a keyword
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> set silhouettes true #1/A
Expected a keyword
> set silhouetteWidth 3
> set silhouetteColor black
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> set silhouettes false
> show silhouettes #1/A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1/A silhouettes
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!2 target m
[Repeated 1 time(s)]
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> hide #!2 target m
> hide #1
> hide #!1 models
> show #1/A
> show cartoons #1/A
Expected ',' or a keyword
> show #!1 models
> hide cartoons #1/A
Expected ',' or a keyword
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> show sel cartoons
> style sel sphere
Changed 4972 atom styles
> style sel stick
Changed 4972 atom styles
> hide sel atoms
> set silhouetteWidth 3
> set silhouetteColor black
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> show #!2 models
> hide #!2 models
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> set silhouettes true
> set silhouetteWidth 2
> set silhouetteColor black
> show #1/C
> hide #!1 models
> show #!2 models
> show #!3 models
> show #2/B
> hide #2/B
> select #2/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #e9fbffff
> hide #!3 models
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency #1 80 All
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency #2 80 All
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency #2/C 0 All
> transparency #2/L 0 All
> select #2/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> color (#!2 & sel) #befbffff
> color (#!2 & sel) #bee6ffff
> color (#!2 & sel) #bee6beff
> transparency #2/A 80 All
> hide #!2 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> transparency #3 80 All
> select #3/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency #3/C 0 All
> transparency #3/L 0 All
> select #3/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> color sel #bfd3b5ff
> color sel #96b27eff
> select #3/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> color (#!3 & sel) #f2b27eff
> color (#!3 & sel) #f2bf7eff
> color (#!3 & sel) #f2bfc7ff
> select #3/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency #3/A 80 All
> show #!2 models
> show #!1 models
> select #3/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> hide sel cartoons
> select #2/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> hide sel cartoons
> select #3/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> hide sel cartoons
> surface sel
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> surface (#!1 & sel)
> select #2/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> surface sel
> select #3/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> surface sel
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 90
> cartoon (#!1 & sel)
[Repeated 1 time(s)]
> surface hidePatches (#!1 & sel)
> set silhouettes true
> set silhouetteWidth 3
> set silhouetteColor black
> cartoon
> surface
> surface style solid
> surface mode transparent
Expected an atoms specifier or a keyword
> transparency 50,surface
Missing or invalid "percent" argument: Expected a number
> cartoon
> transparency 95,surface
Missing or invalid "percent" argument: Expected a number
> transparency (#!1 & sel) 90
> surface style mesh
> surface smoothness 3
Expected an atoms specifier or a keyword
> surface style #1.3 solid
> surface style solid
> set depthCue false
Expected a keyword
> cartoon front
Expected an atoms specifier or a keyword
> transparency 90,surface
Missing or invalid "percent" argument: Expected a number
> select all
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 6 models selected
> show sel cartoons
[Repeated 1 time(s)]
> cartoon (#!1-3 & sel)
> hide sel surfaces
> show sel surfaces
[Repeated 1 time(s)]
> hide sel surfaces
> hide sel cartoons
> show sel surfaces
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> show sel cartoons
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> transparency #3/A 10 All
> transparency #3/A 80 All
> cartoon_transparency #3/A 0 all
Unknown command: cartoon_transparency #3/A 0 all
> show sel cartoons
[Repeated 2 time(s)]
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #2/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #3/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> surface hidePatches (#!3 & sel)
> hide surfaces
> show surfaces
> show cartoons
> transparency 80,surface
Missing or invalid "percent" argument: Expected a number
> cartoon
> transparency 70
> transparency 90
> show models
> cartoon
> surface style #3.4 dot
> select all
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 6 models selected
> surface style mesh
> cartoon
> surface smoothness 3
Expected an atoms specifier or a keyword
> surface smoothness 1
Expected an atoms specifier or a keyword
> surface style solid
> hide surfaces
> color white,surface
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color white,s
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color white, bysurface
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color white sorface
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white surfaces
> show surfaces
> select up
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 15 models selected
> select up
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 15 models selected
> select up
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 15 models selected
> select up
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 15 models selected
> select up
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 15 models selected
> select down
6 pseudobonds, 12 models selected
> select down
6 pseudobonds, 3 models selected
> select down
6 pseudobonds, 3 models selected
> select up
10633 atoms, 6 pseudobonds, 672 residues, 7 models selected
> select up
10706 atoms, 10836 bonds, 6 pseudobonds, 674 residues, 7 models selected
> select up
16046 atoms, 10836 bonds, 6 pseudobonds, 1346 residues, 11 models selected
> transparency 70
> show cartoons
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> hide cartoons
> show cartoons
> hide surfaces
> hide #!3 models
> hide #!2 models
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> color (#!1 & sel) #f2bfb4ff
> color (#!1 & sel) #f2bfbeff
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> select #3/A
2543 atoms, 2608 bonds, 2 pseudobonds, 322 residues, 2 models selected
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> color (#!3 & sel) #a5bfbeff
> color (#!3 & sel) #a5d2beff
> color (#!3 & sel) #a5d2e6ff
> transparency #3/A 90 All
> transparency #3/A 80 All
> transparency #1/A 90 All
> transparency #1/A 80 All
> transparency #2/A 80 All
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> color #3 #7b7979ff
> undo
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> color #3 #e67979ff
> undo
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> select #3/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> color (#!3 & sel) #e6e679ff
> color (#!3 & sel) #e6e6faff
> transparency #3/B 80 All
> hide #!3 models
> show #!2 models
> select #2/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> color (#!2 & sel) #e6e664ff
> color (#!2 & sel) #e6e6faff
> transparency #2/B 80 All
> show #!1 models
> hide #!2 models
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> color (#!1 & sel) #e6e664ff
> color (#!1 & sel) #e6e6faff
> transparency #1/B 80 All
> transparency #1/C 0 All
> transparency #1/L 0 All
> show #!2 models
> show #!3 models
> transparency #2/L 0 All
> transparency #2/C 0 All
> transparency #1/L 0 All
> transparency #1/C 0 All
> show surfaces
> show sel cartoons
[Repeated 11 time(s)]
> show target cs
> transparency 50,s
Missing or invalid "percent" argument: Expected a number
> transparency 50 target s
> transparency 50 target c
> transparency 0 target c
> transparency 20 target c
> transparency 0 target c
> transparency 90 target s
> transparency 5 target c
> transparency 0 target c
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> hide surfaces
> show target cs
> select #1/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> surface hidePatches (#!1 & sel)
[Repeated 1 time(s)]
> select #3/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> surface hidePatches (#!3 & sel)
> select #3/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> cartoon hide (#!3 & sel)
> select #2/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> cartoon hide (#!2 & sel)
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> cartoon hide (#!1 & sel)
> transparency 95 target s
> transparency 5 target c
> transparency 0 target c
> view #3 clip false
> log metadata #3
No models had metadata
> log chains #3
Chain information for NTSR1-ARRB2-N191.pdb #3
---
Chain | Description
A | No description available
B | No description available
L | No description available
> select #1/A
4972 atoms, 5033 bonds, 2 pseudobonds, 322 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #e6e6fa84
> color (#!1 & sel) #e6e6fa83
> color (#!1 & sel) #e6e6fa7e
> color (#!1 & sel) #e6e6fa80
> color (#!1 & sel) #e6e6fa8a
> color (#!1 & sel) #e6e6fa8b
> color (#!1 & sel) #e6e6fa8f
> color (#!1 & sel) #e6e6fa90
> color (#!1 & sel) #e6e6fa9c
[Repeated 1 time(s)]
> color (#!1 & sel) #e6e6fab9
> color (#!1 & sel) #e6e6fac7
> color (#!1 & sel) #e6e6fac8
> color (#!1 & sel) #e6e6fad6
> color (#!1 & sel) #e6e6fad9
> color (#!1 & sel) #e6e6fadc
> color (#!1 & sel) #e6e6fadd
> color (#!1 & sel) #e6e6fae2
> color (#!1 & sel) #e6e6fae4
> color (#!1 & sel) #e6e6fae6
> color (#!1 & sel) #e6e6fae8
> color (#!1 & sel) #e6e6faed
> color (#!1 & sel) #e6e6faf2
> color (#!1 & sel) #e6e6faf7
> color (#!1 & sel) #e6e6fafa
> color (#!1 & sel) #e6e6fafb
> color (#!1 & sel) #e6e6faff
> color (#!1 & sel) #e6e6fafe
> color (#!1 & sel) #e6e6fad7
> color (#!1 & sel) #e6e6fac8
[Repeated 1 time(s)]
> color (#!1 & sel) #e6e6fac2
> color (#!1 & sel) #e6e6faba
> color (#!1 & sel) #e6e6fab5
> color (#!1 & sel) #e6e6fab4
> color (#!1 & sel) #e6e6fab1
> color (#!1 & sel) #e6e6faad
> color (#!1 & sel) #e6e6faa8
> color (#!1 & sel) #e6e6faa5
> color (#!1 & sel) #e6e6faa1
> color (#!1 & sel) #e6e6fa9e
> color (#!1 & sel) #e6e6fa9b
> color (#!1 & sel) #e6e6fa98
> color (#!1 & sel) #e6e6fa95
> color (#!1 & sel) #e6e6fa93
> color (#!1 & sel) #e6e6fa8f
> color (#!1 & sel) #e6e6fa8d
> color (#!1 & sel) #e6e6fa8c
> color (#!1 & sel) #e6e6fa88
> color (#!1 & sel) #e6e6fa84
> color (#!1 & sel) #e6e6fa81
> color (#!1 & sel) #e6e6fa80
> color (#!1 & sel) #e6aafa80
> color (#!1 & sel) #e6c8fa80
> color (#!1 & sel) #e6d3fa80
> color (#!1 & sel) #f4d3fa80
[Repeated 1 time(s)]
> color (#!1 & sel) #f3d3fa80
> color (#!1 & sel) #f1d3fa80
> color (#!1 & sel) #efd3fa80
> color (#!1 & sel) #eed3fa80
> color (#!1 & sel) #ddd3fa80
[Repeated 2 time(s)]
> color (#!1 & sel) #f2d3fa80
[Repeated 1 time(s)]
> color (#!1 & sel) #f2bffa80
> color (#!1 & sel) #f2bfc780
> color (#!1 & sel) #f2bfc781
> color (#!1 & sel) #f2bfc7ff
> color (#!1 & sel) #f2bfc7d7
> color (#!1 & sel) #f2bfc7cb
> color (#!1 & sel) #f2bfc77c
> transparency 95 target s
> color (#!1 & sel) #f2bfc7ff
> transparency 95 target s
> color (#!1 & sel) #f2bfc7e1
> color (#!1 & sel) #f2bfc7ff
> transparency 95 target s
> color (#!1 & sel) #ffe8ffff
> transparency 95 target s
> color (#!1 & sel) #f2e8ffff
> color (#!1 & sel) #f2bfffff
> color (#!1 & sel) #f2bfc7ff
> transparency 95 target s
> transparency 5 target c
> transparency 95 target s
> transparency 100 target s
> transparency 95 target s
> show target cs
> hide #!2 models
> hide #!3 models
> hide target s
> select up
10706 atoms, 10836 bonds, 2 pseudobonds, 674 residues, 3 models selected
> show #!2 models
> show #!3 models
> show target cs
> transparency 5 target c
> transparency 0 target c
> select #1/B
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> cartoon hide (#!1 & sel)
> select #2/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> cartoon hide (#!2 & sel)
> select #3/B
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> cartoon hide (#!3 & sel)
> save 1.png supersample 4
> cd Desktop
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> log
> save /Users/ruidi/Desktop/1.png supersample 4
> transparency 5 target c
> save /Users/ruidi/Desktop/2.png supersample 4
> transparency 0 target c
> transparency 80 target c
> hide surfaces
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface sel
> hide #!2 models
> hide #!3 models
> transparency 90 target c
> select ~sel & ##selected
10673 atoms, 10799 bonds, 2 pseudobonds, 673 residues, 2 models selected
> select ~sel & ##selected
33 atoms, 37 bonds, 1 residue, 1 model selected
> select down
4972 atoms, 5033 bonds, 322 residues, 2 models selected
> save /Users/ruidi/Desktop/3.png supersample 4
[Repeated 1 time(s)]
> show #!2 models
> hide #!1 models
> select up
10706 atoms, 10836 bonds, 674 residues, 2 models selected
> select up
10706 atoms, 10836 bonds, 2 pseudobonds, 674 residues, 6 models selected
> select down
10706 atoms, 10836 bonds, 674 residues, 5 models selected
> select add #1
10706 atoms, 10836 bonds, 2 pseudobonds, 674 residues, 6 models selected
> select add #2
16122 atoms, 16386 bonds, 4 pseudobonds, 1348 residues, 8 models selected
> select add #3
21495 atoms, 21893 bonds, 6 pseudobonds, 2021 residues, 13 models selected
> select subtract #2
16079 atoms, 16343 bonds, 4 pseudobonds, 1347 residues, 14 models selected
> select subtract #3
10706 atoms, 10836 bonds, 2 pseudobonds, 674 residues, 9 models selected
> select subtract #1
4 models selected
> select add #1
10706 atoms, 10836 bonds, 2 pseudobonds, 674 residues, 2 models selected
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> surface sel
> save /Users/ruidi/Desktop/4.png supersample 4
> hide #!2 models
> show #!3 models
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface sel
> save /Users/ruidi/Desktop/5.png supersample 4
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface hidePatches (#!3 & sel)
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> surface hidePatches (#!2 & sel)
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface hidePatches (#!1 & sel)
> transparency 0 target c
> hide #!3 models
> transparency 10 target c
> select #2/A:413
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface #1-2
> hide surfaces
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface #1-2
> hide surfaces
> show #!3 models
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface (#!3 & sel)
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> surface (#!2 & sel)
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> save
> /Users/ruidi/Desktop/065_ntsr1/analysis_results/crystalanalysis/0227/1.mol2
> hide #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/L #2/L #3/L
Alignment identifier is 1
> sequence chain #1/A #2/A #3/A
Alignment identifier is 2
> sequence chain #1/B #2/B #3/B
Alignment identifier is 3
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/A
Alignment identifier is 2
> select #1/A:414 #2/A:414 #3/A:414
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:382-414 #2/A:382-414 #3/A:382-414
277 atoms, 274 bonds, 3 pseudobonds, 24 residues, 6 models selected
2 [ID: 2] region 3 chains [315-322] RMSD: 4.261
> select #1/A:159 #2/A:159 #3/A:159
30 atoms, 27 bonds, 3 residues, 3 models selected
> select #1/A:152-159 #2/A:152-159 #3/A:152-159
236 atoms, 236 bonds, 24 residues, 3 models selected
2 [ID: 2] region 3 chains [101-108] RMSD: 0.361
> select #1/A:188 #2/A:188 #3/A:188
42 atoms, 42 bonds, 3 residues, 3 models selected
> select #1/A:188-213 #2/A:188-213 #3/A:188-213
786 atoms, 798 bonds, 78 residues, 3 models selected
2 [ID: 2] region 3 chains [137-162] RMSD: 0.687
> select #1/A:414 #2/A:414 #3/A:414
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/A:408-414 #2/A:408-414 #3/A:408-414
242 atoms, 242 bonds, 21 residues, 3 models selected
2 [ID: 2] region 3 chains [316-322] RMSD: 3.697
> show (#!1-2 & sel) target ab
> delete atoms (#!1-2 & sel)
> delete bonds (#!1-2 & sel)
> show #!3 models
> select #3/A:408-409
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/A:408-414
66 atoms, 66 bonds, 7 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> show (#!3 & sel) target ab
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select
> #1/A:60-89,101-129,137-171,173-179,182-206,219-221,230-266,291-327,331-333,336-367,369-379
> #2/A:60-89,101-129,137-171,173-179,182-206,219-221,230-266,291-327,331-333,336-367,369-379
> #3/A:60-89,101-129,137-171,173-179,182-206,219-221,230-266,291-327,331-333,336-367,369-379
7911 atoms, 8037 bonds, 747 residues, 3 models selected
> select #1/A:308 #2/A:308 #3/A:308
30 atoms, 27 bonds, 3 residues, 3 models selected
> select #1/A:308 #2/A:308 #3/A:308
30 atoms, 27 bonds, 3 residues, 3 models selected
2 [ID: 2] region 3 chains [241] RMSD: 0.639
> select
> #1/A:60-89,101-129,137-171,173-179,182-206,219-221,230-266,291-327,331-333,336-367,369-379
> #2/A:60-89,101-129,137-171,173-179,182-206,219-221,230-266,291-327,331-333,336-367,369-379
> #3/A:60-89,101-129,137-171,173-179,182-206,219-221,230-266,291-327,331-333,336-367,369-379
7911 atoms, 8037 bonds, 747 residues, 3 models selected
> select #1/A:305 #2/A:305 #3/A:305
35 atoms, 32 bonds, 3 residues, 3 models selected
> select #1/A:299-305 #2/A:299-305 #3/A:299-305
239 atoms, 239 bonds, 21 residues, 3 models selected
2 [ID: 2] region 3 chains [232-238] RMSD: 1.828
> select #1/A:290 #2/A:290 #3/A:290
35 atoms, 32 bonds, 3 residues, 3 models selected
> select #1/A:284-290 #2/A:284-290 #3/A:284-290
204 atoms, 204 bonds, 21 residues, 3 models selected
2 [ID: 2] region 3 chains [217-223] RMSD: 2.946
> show (#!1-3 & sel) target ab
> hide (#!1-3 & sel) target a
> select #1/A:289 #2/A:289 #3/A:289
20 atoms, 17 bonds, 3 residues, 3 models selected
> select #1/A:284-289 #2/A:284-289 #3/A:284-289
169 atoms, 169 bonds, 18 residues, 3 models selected
2 [ID: 2] region 3 chains [217-222] RMSD: 3.003
> show (#!1-3 & sel) target ab
> delete atoms (#!1-3 & sel)
> delete bonds (#!1-3 & sel)
> hide #!3 models
> focus
Unknown command: focus
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> zoom sel
Expected a number > 0 or a keyword
> zoom #1/C
Expected a number > 0 or a keyword
> select ligand
422 atoms, 437 bonds, 23 residues, 3 models selected
> zoom sel
Expected a number > 0 or a keyword
> zoom
Pixel size at center of rotation is 0.0536
> zoom 2
> camera depth true
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera blur 0.5
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera mono
> camera clip 5 50
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera 360
> camera 0
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera mono
> set depthCue true
Expected a keyword
> camera mono
> graphics quality best
Expected a number or a keyword
> set fog 0.5
Expected a keyword
> set projection perspective
Expected a keyword
> set nearclip 0.5
Expected a keyword
> lighting depthCue true
> lighting depthCueColor gray
> lighting depthCueColor white
> transparency 50 atoms farclip
Expected ',' or a keyword
> transparency 60 atoms farclip
Expected ',' or a keyword
> select @/bfactor>40
Expected an objects specifier or a keyword
> set nearclip 1
Expected a keyword
> lighting depthCueColor gray
> lighting depthCueColor white
> lighting depthCueColor transparency 60
Invalid "depthCueColor" argument: Invalid color name or specifier
> lighting depthCueStart 0.5
> lighting depthCueStart 0.3
> lighting depthCueStart 0.5
> lighting depthCueEnd 1.0
> transparency 50
> transparency 80
> transparency 90
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface (#!1 & sel)
> lighting preset gentle
> lighting preset full
> lighting shadows true
> lighting qualityOfShadows fine
> select
21084 atoms, 21479 bonds, 3 pseudobonds, 1982 residues, 6 models selected
> zoom
Pixel size at center of rotation is 0.0475
> camera mono
> save /Users/ruidi/Desktop/6.png supersample 4
> hide #!2 models
> show #!3 models
> save /Users/ruidi/Desktop/7.png supersample 4
> matchmaker #1/A: resid 182-204 to #2/A: resid 182-204
Expected a keyword
> matchmaker #1/A: resid 182-204 to #2/A: resid 182-204
Expected a keyword
> matchmaker #1/A:182-204 #2/A:182-204
Missing required "to" argument
> matchmaker #1/A:182-204 to #2/A:182-204
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 NTSR1-ARRB2-N065.pdb, chain A (#2) with NTSR1-ARRB2-SBI553.pdb,
chain A (#1), sequence alignment score = 118.4
RMSD between 23 pruned atom pairs is 0.578 angstroms; (across all 23 pairs:
0.578)
> matchmaker #3/A:182-204 to #1/A:182-204
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 NTSR1-ARRB2-SBI553.pdb, chain A (#1) with NTSR1-ARRB2-N191.pdb,
chain A (#3), sequence alignment score = 118.4
RMSD between 23 pruned atom pairs is 0.584 angstroms; (across all 23 pairs:
0.584)
> matchmaker #2/A:182-204 to #1/A:182-204
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 NTSR1-ARRB2-SBI553.pdb, chain A (#1) with NTSR1-ARRB2-N065.pdb,
chain A (#2), sequence alignment score = 118.4
RMSD between 23 pruned atom pairs is 0.578 angstroms; (across all 23 pairs:
0.578)
> show #!2 models
> matchmaker #2/A:182-204 to #1/A:182-204
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 NTSR1-ARRB2-SBI553.pdb, chain A (#1) with NTSR1-ARRB2-N065.pdb,
chain A (#2), sequence alignment score = 118.4
RMSD between 23 pruned atom pairs is 0.578 angstroms; (across all 23 pairs:
0.578)
> hide #!3 models
> save /Users/ruidi/Desktop/8.png supersample 4
> hide #!2 models
> show #!3 models
> save /Users/ruidi/Desktop/9.png supersample 4
> camera mono
> save /Users/ruidi/Desktop/9.png supersample 4
> hide #!3 models
> show #!2 models
> save /Users/ruidi/Desktop/8.png supersample 4
> show #!3 models
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> hide #!2 models
> hide #!3 models
> contacts #1/C 5
Expected a keyword
> contacts #1/C:SRW 5
Expected a keyword
> contacts #1/A 5
Expected a keyword
> contacts #1/A:LIG 5
Expected a keyword
Unsupported scale factor (0.000000) detected on Display0
[Repeated 19 time(s)]
> show #!2 models
> show #!3 models
> select ::name="PIO"
80 atoms, 80 bonds, 2 residues, 2 models selected
> style sel stick
Changed 80 atom styles
> select ::name="PIO"
80 atoms, 80 bonds, 2 residues, 2 models selected
> show sel target ab
> select ::name="PIO"
80 atoms, 80 bonds, 2 residues, 2 models selected
> color sel byhetero
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> save
> /Users/ruidi/Desktop/065_ntsr1/analysis_results/crystalanalysis/0227/0304.cxs
——— End of log from Tue Mar 4 14:50:56 2025 ———
opened ChimeraX session
> show #!1 models
> show #!3 models
> close session
> open "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N191 model _R-lig-
> coot-4.pdb"
Chain information for NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb #1
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
> open "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N065 model
> -coot-9-2.pdb"
Chain information for NTSR1-ARRB2-N065 model -coot-9-2.pdb #2
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
> open "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2 C1 model
> J4765_arrestin2-coot-1.pdb"
Chain information for NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb #3
---
Chain | Description
B | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
> style sphere
Changed 34157 atom styles
> style sphere
Changed 34157 atom styles
> style sphere
Changed 34157 atom styles
> style stick
Changed 34157 atom styles
> style ball
Changed 34157 atom styles
> style ball
Changed 34157 atom styles
> style sphere
Changed 34157 atom styles
> style ball
Changed 34157 atom styles
> style stick
Changed 34157 atom styles
> show cartoons
Computing secondary structure
[Repeated 2 time(s)]
> hide atoms
> matchmaker #1/B to #2/E
No molecules/chains to match specified
> matchmaker #1/E to #2/E
Computing secondary structure
[Repeated 1 time(s)] 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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain E (#2) with
NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb, chain E (#1), sequence alignment
score = 1637.8
RMSD between 302 pruned atom pairs is 0.713 angstroms; (across all 322 pairs:
1.077)
> select ~sel & ##selected
Nothing selected
> matchmaker #3/B to #2/E
Computing secondary structure
[Repeated 1 time(s)] 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 NTSR1-ARRB2-N065 model -coot-9-2.pdb, chain E (#2) with NTSR1-ARRB2
C1 model J4765_arrestin2-coot-1.pdb, chain B (#3), sequence alignment score =
1561.6
RMSD between 280 pruned atom pairs is 0.760 angstroms; (across all 322 pairs:
1.539)
> select ~sel & ##selected
Nothing selected
> select #1/L#2/L#3/L
240 atoms, 243 bonds, 18 residues, 3 models selected
> select #1/E#2/E#3/E
10656 atoms, 10854 bonds, 4 pseudobonds, 989 residues, 5 models selected
> select #1/Q#2/Q#3/Q
6071 atoms, 6173 bonds, 648 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> select #1/D#2/D#3/D
6591 atoms, 6720 bonds, 663 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> show cartoons
[Repeated 1 time(s)]
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select #1/E#2/E#3/E
10656 atoms, 10854 bonds, 4 pseudobonds, 989 residues, 5 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/E #2/E #3/B
Alignment identifier is 1
> select #1/E:414 #2/E:414 #3/B:414
33 atoms, 30 bonds, 3 residues, 3 models selected
> select #1/E:52-414 #2/E #3/B
10058 atoms, 10249 bonds, 6 pseudobonds, 966 residues, 6 models selected
1 [ID: 1] region 3 chains [1-322] RMSD: 1.368
> set bgColor white
> lighting soft
> lighting simple
> lighting full
> lighting simple
> ui tool show "Selection Inspector"
> select ~sel & ##selected
11437 atoms, 11644 bonds, 1055 residues, 3 models selected
> rename #1 NTSR1-ARRB2-N191.pdb
> select #1/E
2576 atoms, 2645 bonds, 2 pseudobonds, 323 residues, 2 models selected
> rename #2 NTSR1-ARRB2-N065.pdb
> rename #3 NTSR1-ARRB2-SBI553.pdb
> select #3/E
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> select #3/E
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> select #3/E
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> select #3/E
5537 atoms, 5601 bonds, 344 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A
2739 atoms, 2803 bonds, 344 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 21 residues
> delete atoms sel
> delete bonds sel
Drag select of 21 residues, 3 pseudobonds
Drag select of 12 residues, 2 pseudobonds
> delete atoms (#!1-3 & sel)
> delete bonds (#!1-3 & sel)
> select #3/B:288
17 atoms, 16 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/E:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/E:288
14 atoms, 12 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="LIG"
69 atoms, 77 bonds, 2 residues, 2 models selected
> style sel stick
Changed 69 atom styles
> select ::name="LIG"
69 atoms, 77 bonds, 2 residues, 2 models selected
> show sel target ab
> select ::name="SRW"
33 atoms, 37 bonds, 1 residue, 1 model selected
> show sel target ab
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> changechains #1:.E A
No residues specified have any of the 'from' chain IDs
> changechains #1/E A
Chain IDs of 311 residues changed
> hide #!1 models
> hide #!3 models
> changechains #2/E A
Chain IDs of 310 residues changed
> hide #!2 models
> show #!3 models
> changechains #3/B A
Chain IDs of 310 residues changed
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> changechains #3/B: resn LIG, C
Chain ID argument must either two lists of IDs, or one single ID
> changechains #3/B: LIG, C
Missing or invalid "fromIds" argument: Expected a text string
> pdbrun @501.A chain A C
Unknown command: pdbrun @501.A chain A C
> pdbrun @501.A C
Unknown command: pdbrun @501.A C
> pdbrun #1/ @501 .C
Unknown command: pdbrun #1/ @501 .C
> pdbrun #1/ 501 C
Unknown command: pdbrun #1/ 501 C
> pdbrun #1/ A:501 C
Unknown command: pdbrun #1/ A:501 C
> select #2:501.A
Expected an objects specifier or a keyword
> pdbrun @501.A chain A C
Unknown command: pdbrun @501.A chain A C
> pdbrun #1/A/501 C
Unknown command: pdbrun #1/A/501 C
> pdbrun #1/A:501 C
Unknown command: pdbrun #1/A:501 C
> pdbrun #1/A:@501 C
Unknown command: pdbrun #1/A:@501 C
> pdbrun #1/A/.501 C
Unknown command: pdbrun #1/A/.501 C
> pdbrun #1/A:501 TO C
Unknown command: pdbrun #1/A:501 TO C
> pdbrun #1/A:501 to C
Unknown command: pdbrun #1/A:501 to C
> pdbrun #1/A:resid 501 C
Unknown command: pdbrun #1/A:resid 501 C
> ui tool show "Change Chain IDs"
> select #1/A:resid 501
Expected a keyword
> select #1/A:LIG
33 atoms, 37 bonds, 1 residue, 1 model selected
> pdbrun #1/A:LIG C
Unknown command: pdbrun #1/A:LIG C
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 1 residues changed
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> select #1/A
2439 atoms, 2503 bonds, 1 pseudobond, 310 residues, 2 models selected
> select #3/A
4789 atoms, 4849 bonds, 1 pseudobond, 310 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!3 & sel) #01ffffff
> color (#!3 & sel) #f3ffffff
> color (#!3 & sel) #f2ffffff
> color (#!3 & sel) #f2bfffff
[Repeated 1 time(s)]
> color (#!3 & sel) #f2bfc7ff
[Repeated 1 time(s)]
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> select #3/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> color sel #19bfc7ff
> color sel #19b8c7ff
> color sel #19b8b7ff
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel #00b8b7ff
> color sel #19b8b7ff
> color sel #19b8b4ff
> color sel #19b8b7ff
> color sel byhetero
> color sel #19b5b7ff target s
> color sel #19b8b7ff target s
> color sel #19b8b6ff target s
> color sel #19b8b7ff target s
> select clear
> select #3/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> toolshed show
Downloading bundle MolecularDynamicsViewer-1.6-py3-none-any.whl
Installed MolecularDynamicsViewer (1.6)
QWebEngineUrlScheme::registerScheme: Too late to register scheme "kmd"
Downloading bundle ChimeraX_LigandRecognizer-0.2-py3-none-any.whl
Installed ChimeraX-LigandRecognizer (0.2)
Downloading bundle ChimeraX_AllMetal3D-0.8-py3-none-any.whl
Installed ChimeraX-AllMetal3D (0.8)
Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl
Installed ChimeraX-Cytoscape (0.1)
Downloading bundle ChimeraX_NIHPresets-1.2.7-py3-none-any.whl
Installed ChimeraX-NIHPresets (1.2.7)
Downloading bundle ChimeraX_NMRSTAR-1.0.2-py3-none-any.whl
Deferring bundle installation
> select #3/L & zone sel <5
Expected a keyword
> select #3/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> zone sel <5
Expected a keyword
> select zone #3/L<5
Missing or invalid "near" argument: only initial part "#3/L" of atom specifier
valid
> select #3/L zr<5
Expected a keyword
> select #3/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> select zone sel <5
Missing or invalid "range" argument: Expected a number
> select zone #3/L 5
Selected 634 atoms
> show sel
> hide sel
> show surfaces
> hide surfaces
> surface sel
> transparency (#!3 & sel) 60
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface sel
> transparency (#!3 & sel) 60
> transparency (#!3 & sel) 40
> transparency (#!3 & sel) 80
> select zll
Expected an objects specifier or a keyword
> select all
10089 atoms, 10292 bonds, 3 pseudobonds, 953 residues, 6 models selected
> transparency (#!3 & sel) 80
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> select zone #3/L 5 restrict #3
Expected an objects specifier or a keyword
> select zone #3/L 5 & #3.1
Expected an objects specifier or a keyword
> select #3/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> select (zone #3/L 5) & #3
Expected an objects specifier or a keyword
> select extend 5 restrict #3
Expected an objects specifier or a keyword
> list
Unknown command: modelcif list
> select contacts #3/L 5 restrict #3
Expected an objects specifier or a keyword
> select contacts #3/L 5 & #3
Expected an objects specifier or a keyword
> select contacts #3/L 5 & #3
Expected an objects specifier or a keyword
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> select #1/A
2439 atoms, 2503 bonds, 1 pseudobond, 310 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #a5b8b7ff target s
> color (#!1 & sel) #a5d2b7ff target s
> color (#!1 & sel) #a5d2e6ff target s
> color (#!1 & sel) #a5d2d2ff target acsp
> color (#!1 & sel) #a5d2e6ff target acsp
> select #1/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> color (#!1 & sel) #96d2e6ff target acsp
> color (#!1 & sel) #96b2e6ff target acsp
> color (#!1 & sel) #96b27eff target acsp
> hide surfaces sele
Expected ',' or a keyword
> hide surfaces
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> color sel byhetero target acsp
> color sel #96b278ff target acsp
> color sel #96b27eff target acsp
> color sel byhetero target acp
> surface sel
> select zone #1/L 5
Selected 625 atoms
> surface sel
> transparency (#!1 & sel) 80
> select all
10089 atoms, 10292 bonds, 3 pseudobonds, 953 residues, 6 models selected
> transparency (#!1 & sel) 80
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> hide surfaces
> select #2/A
2439 atoms, 2503 bonds, 1 pseudobond, 310 residues, 2 models selected
> select #2/A
2439 atoms, 2503 bonds, 1 pseudobond, 310 residues, 2 models selected
> color (#!2 & sel) #beb27eff target acp
> color (#!2 & sel) #bee67eff target acp
> color (#!2 & sel) #bee6beff target acp
> select #2/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> color (#!2 & sel) #ffe6beff target acp
> color (#!2 & sel) #ffa0beff target acp
> color (#!2 & sel) #ffa07aff target acp
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> color sel #ffa078ff target acp
> color sel #ffa07aff target acp
> color sel #ffa078ff target acsp
> color sel #ffa07aff target acsp
> color sel byhetero target acp
> select zone #2/L 5
Selected 657 atoms
> surface sel
> select #2/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> color (#!2 & sel) #ffa078ff target acsp
> color (#!2 & sel) #ffa07aff target acsp
> select #2/A
2439 atoms, 2503 bonds, 1 pseudobond, 310 residues, 2 models selected
> color (#!2 & sel) #bea07aff target acsp
> color (#!2 & sel) #bee67aff target acsp
> color (#!2 & sel) #bee6beff target acsp
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> show sel
> surface sel
> select all
10089 atoms, 10292 bonds, 3 pseudobonds, 953 residues, 6 models selected
> transparency (#!2 & sel) 80
> show #!3 models
> show #!1 models
> select all
10089 atoms, 10292 bonds, 3 pseudobonds, 953 residues, 6 models selected
> transparency (#!1-3 & sel) 80
> select chain L
Expected an objects specifier or a keyword
> select #1/chain L
Expected a keyword
> select L
Expected an objects specifier or a keyword
> select #1/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> hide surfaces
> select zone #2/L 5
Selected 657 atoms
> surface sel
> select zone #1/L 5
Selected 625 atoms
> surface sel
> select zone #3/L 5
Selected 634 atoms
> surface sel
> select #1/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> hide surfaces sel
Expected ',' or a keyword
> surface hidePatches sel
> select #2/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> surface hidePatches sel
> select #3/L
124 atoms, 125 bonds, 6 residues, 1 model selected
> surface hidePatches sel
> select #2/C
36 atoms, 40 bonds, 1 residue, 1 model selected
> show surfaces sele
Expected ',' or a keyword
> show surfaces sel
Expected ',' or a keyword
> surface showPatches sele
Expected an objects specifier or a keyword
> surface sele
Expected an atoms specifier or a keyword
> surface sel
> select #1/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface sel
> select #3/C
33 atoms, 37 bonds, 1 residue, 1 model selected
> surface sel
>
Missing command
>
Missing command
>
Missing command
>
Missing command
>
Missing command
>
Missing command
>
Missing command
>
Missing command
> help matchmaker
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/help_viewer/cmd.py", line 81, in help
url = cli.command_url(cmd_name)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3350, in command_url
return _get_help_url(cmd.command_name.split())
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
AttributeError: 'NoneType' object has no attribute 'split'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3350, in command_url
return _get_help_url(cmd.command_name.split())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> align #3/A:182-204 toAtoms #1/A:182-204
Unequal number of atoms to pair, 384 and 180
> align #3/A:182-204， #1/A:182-204
Missing or invalid "atoms" argument: only initial part "#3/A:182-204" of atom
specifier valid
> align #3/A:182-204 toAtoms #1/A:182-204
Unequal number of atoms to pair, 384 and 180
> align #3/A:182-204 toAtoms #1/A:182-204 pair ca
Expected a keyword
> select H
2466 atoms, 316 residues, 1 model selected
> align #3/A:182-204@!H to #1/A:182-204@!H
Missing or invalid "atoms" argument: only initial part "#3/A:182-204" of atom
specifier valid
> align #3/A:182-204 toAtoms #1/A:182-204 pair ca
Expected a keyword
> select #3/A:182-204 & @CA
23 atoms, 23 residues, 1 model selected
> select #1/A:182-204 & @CA
23 atoms, 23 residues, 1 model selected
> align sel
Missing required "to_atoms" argument
>
Missing command
> align #3/A:182-204 toAtoms #1/A:182-204 pair ca
Expected a keyword
> delete sidechain & H
> align #3/A:182-204 toAtoms #1/A:182-204
Unequal number of atoms to pair, 202 and 180
> module check
Unknown command: module check
> toolshed list
List of installed bundles:
* AddCharge (1.5.18): Add partial charges to atoms
* AddH (2.2.6): Add hydrogens
* AlignmentAlgorithms (2.0.2): Sequence alignment algorithms
* AlignmentHdrs (3.5): Alignment header support
* AlignmentMatrices (2.1): Sequence alignment similarity matrices
* Alignments (2.16.1): Sequence alignment support
* AllMetal3D (0.8): AllMetal3D: Predict metal and water binding sites in proteins
* AlphaFold (1.0.1): Predict or fetch AlphaFold structures
* AltlocExplorer (1.1.2): Examine/change alternate atomic locations
* AmberInfo (1.0): Provide information about AmberTools installation
* Arrays (1.1): C++ library for parsing numpy arrays
* Atomic (1.58.8): Atomic-structure functionality
* AtomicLibrary (14.1.11): Atomic-structure C++ library
* AtomSearch (2.0.1): 3D atom search
* AxesPlanes (2.4): Depict axes or planes
* BasicActions (1.1.2): Basic actions for user-defined specifier names
* BILD (1.0): BILD file reader
* BlastProtein (3.0.0): Search PDB/NR/AlphaFold using BLAST
* BondRot (2.0.4): Bond rotation support
* BugReporter (1.0.1): Report bugs when an error occurs
* BuildStructure (2.13.1): Create/modify structures
* Bumps (1.0): Find protrusions in density maps
* ButtonPanel (1.0.1): Create custom user interface panels
* CageBuilder (1.0.1): Build polygonal meshes for oligomeric molecular assemblies
* CellPack (1.0): Fetch cellPACK models from web
* Centroids (1.4): Depict centroid of atoms
* ChangeChains (1.1): Change chain IDs
* CheckWaters (1.4): Check water placement in maps
* ChemGroup (2.0.1): Detect chemically functional groups
* Clashes (2.3): Find clashes/contacts in structures
* ColorActions (1.0.5): Simple interface for coloring objects
* ColorGlobe (1.0): Show directional resolution colored sphere
* ColorKey (1.5.6): Add color key to graphics
* CommandLine (1.2.5): Command line support
* ConnectStructure (2.0.1): Add bonds to structures that lack them
* Contacts (1.0.1): Display chain contact maps
* Core (1.9): ChimeraX Core Package
* CoreFormats (1.2): ChimeraX session support
* coulombic (1.4.4): Compute/show electrostatic potential
* Crosslinks (1.0): Analyze crosslinks
* Crystal (1.0): Crystal symmetries
* CrystalContacts (1.0.1): Show contacting asymmetric units in a crystal
* Cytoscape (0.1): Cytoscape interface
* DataFormats (1.2.3): Data format management
* Dicom (1.2.6): Read medical imaging and segmentations in DICOM format
* DistMonitor (1.4.2): Interactive distance display
* DockPrep (1.1.3): Prepare structures for docking
* Dssp (2.0): Compute/assign secondary structure
* EMDB-SFF (1.0): EMDB SFF file reader
* ESMFold (1.0): Predict or fetch ESMFold structures
* FileHistory (1.0.1): File History Panel
* FunctionKey (1.0.1): Assign function keys to run commands
* Geometry (1.3): Vector and coordinate system routines
* gltf (1.0): Read/write glTF 3d scene files
* Graphics (1.4.1): OpenGL graphics rendering
* Hbonds (2.5): Identify hydrogen bonds in and among structures
* Help (1.3): Show ChimeraX Help
* HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
* IHM (1.1): Integrative Hybrid Models file reader
* ImageFormats (1.2): Support for saving images
* IMOD (1.0): IMOD model file reader
* IO (1.0.3): Python convenience input/output functions
* ItemsInspection (1.0.1): Inspection of attributes of a set of items
* IUPAC (1.0): IUPAC fetch
* KVFinder (1.2.1): Find cavities/pockets
* Label (1.1.14): Add text labels to graphics
* LigandRecognizer (0.2): This tool uses a PDB model (.pdb or .cif) and corresponding density map (.cpp4) to validate/identify ligands.
* ListInfo (1.2.2): Report attributes for selected atomic data
* Log (1.2): Log support
* LookingGlass (1.1): LookingGlass holographic display
* Maestro (1.9.1): Maestro reader
* Map (1.3): Density maps
* MapData (2.0): Volume data file formats
* MapEraser (1.0.1): Map eraser
* MapFilter (2.0.1): Operations on maps
* MapFit (2.0): Fit molecules into maps
* MapSeries (2.1.1): Volume series
* Markers (1.0.1): Place markers on density maps
* Mask (1.0.2): Mask a volume to a surface
* MatchMaker (2.1.6): Superimpose structures
* MCopy (1.0): Copy atomic structure attributes to another structure
* MDcrds (2.7.2): Molecular dynamics support
* MedicalToolbar (1.1): Toolbar for medical image analysis
* Meeting (1.0.1): Shared interactive VR sessions.
* MLP (1.1.1): Molecular lipophilicity calculation
* mmCIF (2.14.2): mmCIF format read/write
* MMTF (2.2): MMTF format read/write
* ModelArchive (1.0): Fetch structures from Model Archive and display PAE plots
* Modeller (1.5.18): Interface to Modeller
* ModelPanel (1.5): ChimeraX Model Panel
* ModelSeries (1.0.1): Display sequences of models one by one
* Mol2 (2.0.3): Mol2 reader/writer
* Mole (1.0): Open JSON tunnel files from Mole
* MolecularDynamicsViewer (1.6): A UI tool for loading and viewing a multiframe pdb file
* Morph (1.0.2): Morph atomic structures
* MouseModes (1.2): Provide right button mouse mode tool
* Movie (1.0): Commands to record movies
* MutationScores (1.0): Visualize deep mutational scanning data
* Neuron (1.0): Read SWC neuron trace files
* Nifti (1.2): Read medical images in NIfTI format
* NIHPresets (1.2.7): NIH3D presets
* NMRSTAR (1.0.2): Read NMR distance restraints from NMR-STAR files
* NRRD (1.2): Read medical images in NRRD format
* Nucleotides (2.0.3): Create nucleotide-specific displays
* OpenCommand (1.14): Manages 'open' command extensibility
* OrthoPick (1.0.1): Show orthogonal views for tomogram particle picking
* PDB (2.7.6): PDB format read/write
* PDBBio (1.0.1): PDB biological assembly fetch
* PDBLibrary (1.0.4): C++ PDB support
* PDBMatrices (1.0): Crystal and biological unit matrices
* PickBlobs (1.0.1): Measure and color blobs
* Positions (1.0): Read and write model position matrices
* PresetMgr (1.1.2): Preset management
* PubChem (2.2): PubChem fetch
* ReadPbonds (1.0.1): Read in pseudobonds from a file
* Registration (1.1.2): Register ChimeraX
* RemoteControl (1.0): Control ChimeraX from other apps
* RenderByAttr (1.6.2): Depict attribute values on structures
* RenumberResidues (1.1): Renumber residues
* ResidueFit (1.0.1): Display fit of residues to density map
* RestServer (1.3.1): Starts REST server to execute commands from network requests
* RNALayout (1.0): Make RNA models
* RotamerLibMgr (4.0): Manage rotamer libraries
* RotamerLibsDunbrack (2.0): Dunbrack rotamer library
* RotamerLibsDynameomics (2.0): Dynameomics rotamer library
* RotamerLibsRichardson (2.0): Richardson rotamer libraries
* SaveCommand (1.5.1): Manages 'save' command extensibility
* SchemeMgr (1.0): HTTP scheme management
* SDF (2.0.2): SDF file reader
* Segger (1.0): Segment map
* Segment (1.0.1): Watershed segment calculation
* Segmentations (3.5.6): Segment any volume data
* SelInspector (1.0): Inspect contents of selection
* SeqView (2.14): Sequence viewer
* Shape (1.0.1): Make models for geometric shapes
* Shell (1.0.1): Interactive Python shell
* Shortcuts (1.2.0): Button and keyboard shortcuts
* ShowSequences (1.0.3): Choose/show structure sequences
* SideView (1.0.1): Side view of scene
* SimilarStructures (1.0.1): Visualize similar structures found using Foldseek, MMseqs2 or BLAST
* Smiles (2.1.2): SMILES fetch
* SmoothLines (1.0): Smooth network of lines
* SpaceNavigator (1.0): Space Navigator device support
* StdCommands (1.18.1): Standard commands
* STL (1.0.1): STL file read/write
* Storm (1.0): STORM file reader
* StructMeasure (1.2.1): Structure measurement user interface
* Struts (1.0.1): struts for 3D printing
* Surface (1.0.1): Surface calculations
* SwapAA (2.0.1): Swap amino acid
* SwapRes (2.5): Swap residue side chains
* TapeMeasure (1.0): Tape measure mouse mode
* TaskManager (1.0): Manage background tasks in ChimeraX
* Test (1.0): simple regression test
* Toolbar (1.2.3): Toolbar
* ToolshedUtils (1.2.4): Toolshed bundle utilities
* Topography (1.0): Show a topographic surface for a 2D image
* ToQuest (1.0): Copy scenes to VR Quest headset
* Tug (1.0.1): Tug on atoms with molecular dynamics
* UI (1.41): ChimeraX user interface
* Umap (1.0): Utilities for installing and using UMAP
* uniprot (2.3.1): UniProt database support
* UnitCell (1.0.1): Show crystal unit cell
* ViewDockX (1.4.4): Analyze ligand-receptor docking results
* VIPERdb (1.0): Read Virus Particle Explorer .vdb files
* Vive (1.1): Virtual reality headset support
* VolumeMenu (1.0.1): Volume menu
* vrml (1.0): Write basic VRML output for 3D color printing
* VTK (1.0): Legacy VTK file reader and writer
* WavefrontOBJ (1.0): Wavefront OBJ file read/write
* WebCam (1.0.2): Combine camera video with graphics
* WebServices (1.1.4): Web service and HTTP request support
* Zone (1.0.1): Mouse mode to show atom and map zones
> toolshed show
> info tools
Expected a models specifier or a keyword
> usage matchmaker
> help matchmaker
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/help_viewer/cmd.py", line 81, in help
url = cli.command_url(cmd_name)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3350, in command_url
return _get_help_url(cmd.command_name.split())
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
AttributeError: 'NoneType' object has no attribute 'split'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3350, in command_url
return _get_help_url(cmd.command_name.split())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> help align
> align #3/A:182-204 toAtoms #1/A:182-204
Unequal number of atoms to pair, 202 and 180
> align #3/A:180-202 toAtoms #1/A:180-202
Unequal number of atoms to pair, 200 and 178
> align #3/A:182-204@CA toAtoms #1/A:182-204@CA
RMSD between 23 atom pairs is 0.584 angstroms
> transparency 50 target cartoon
Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl
> transparency 50 target cartoon
Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbmpfl
> transparency 50 cartoons
> transparency 60 cartoons
> set silhouettes true
> set silhouetteWidth 3
> set silhouetteColor black
> select all
7932 atoms, 8135 bonds, 3 pseudobonds, 953 residues, 6 models selected
> transparency (#!1-3 & sel) 70
> transparency (#!1-3 & sel) 90
> select #1/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> transparency 60 cartoons sel
Expected ',' or a keyword
> transparency sel 60 cartoons
> transparency sel 0 cartoons
> select #2/L
58 atoms, 59 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> select #3/L
65 atoms, 66 bonds, 6 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> cd /Users/ruidi/Desktop/065_ntsr1/
Current working directory is: /Users/ruidi/Desktop/065_ntsr1
> ls -larth
Unknown command: ls -larth
> ls -larthls
Unknown command: ls -larthls
> ls
Unknown command: ls
> save my_0318_withnts.png width 4000 height 3000
> save my_0318_withnts.png width 6000 height 6000
> graphics quality high
Expected a number or a keyword
> save my_figure.png width 4000 height 3000 supersample 3
> save my_figure.png width 4000 height 4000 supersample 3
> set shadows true
Expected a keyword
> set ambient_occlusion true
Expected a keyword
> lighting gentle
> lighting soft
> lighting simple
> lighting bright
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> set silhouettes
Missing "silhouettes" keyword's argument
> background color white
Unknown command: background color white
> set depth_cue true
Expected a keyword
> set fieldOfView 50
Expected a keyword
> set projection orthographic
Expected a keyword
> camera fieldOfView 50
> camera projection perspective
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera projection ortho
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera projection mono
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera mode ortho
Expected one of '360', '360sbs', '360tb', 'crosseye', 'dome', 'mono', 'ortho',
'sbs', 'stereo', 'tb', or 'walleye' or a keyword
> camera ortho
> camera mono
> camera fieldOfView 50
> select #1/A
2439 atoms, 2503 bonds, 1 pseudobond, 310 residues, 2 models selected
> transparency sel 50 cartoons
> select #2/A
2439 atoms, 2503 bonds, 1 pseudobond, 310 residues, 2 models selected
> transparency sel 50 cartoons
> select #3/A
2691 atoms, 2751 bonds, 1 pseudobond, 310 residues, 2 models selected
> transparency sel 50 cartoons
> set projection perspective
Expected a keyword
> lighting depthCue true
> lighting depthCueColor gray
> lighting depthCueStart 0.3
> lighting depthCueEnd 0.9
> lighting preset gentle
> lighting soft
> lighting simple
> lighting shadows true
> lighting qualityOfShadows fine
> graphics quality best
Expected a number or a keyword
> graphics quality 300
> graphics quality 2
> graphics silhouettes true color black width 3
> graphics rate true maxFrameRate 120
> save withnts.png width W height H supersample S transparentBackground true
Invalid "width" argument: Expected an integer
> save withnts.png width 6000 height 6000 supersample 4 transparentBackground
> true
> save withnts.png width 6000 height 6000 supersample 4
> save withnts.png width 4000 height 3000 supersample 3
> save withnts.png width 6000 height 6000 supersample 3
> save
> /Users/ruidi/Desktop/065_ntsr1/analysis_results/withnts_conformation.cxs
[Repeated 1 time(s)]
> close session
> open
> /Users/ruidi/Desktop/065_ntsr1/analysis_results/conformation_analysis/065_nonts.pdb
> /Users/ruidi/Desktop/065_ntsr1/analysis_results/conformation_analysis/191_nonts.pdb
> /Users/ruidi/Desktop/065_ntsr1/analysis_results/conformation_analysis/sbi553_nonts.pdb
Chain information for 065_nonts.pdb #1
---
Chain | Description
A | No description available
Chain information for 191_nonts.pdb #2
---
Chain | Description
? | No description available
Chain information for sbi553_nonts.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 2 time(s)]
> select #2
2643 atoms, 2714 bonds, 332 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel A
Chain IDs of 332 residues changed
> align #3/A:180-202 toAtoms #1/A:180-202
RMSD between 179 atom pairs is 1.605 angstroms
> align #2/A:180-202 toAtoms #1/A:180-202
RMSD between 179 atom pairs is 1.334 angstroms
> align #2/A:87-120 toAtoms #1/A:87-120
RMSD between 261 atom pairs is 1.290 angstroms
> align #3/A:87-120 toAtoms #1/A:87-120
RMSD between 261 atom pairs is 1.381 angstroms
> close session
> open "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2 C1 model
> J4765_arrestin2-coot-1.pdb"
> "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N065 model
> -coot-9-2.pdb" "/Users/ruidi/Desktop/065_ntsr1/pdb_191/NTSR1-ARRB2-N191
> model _R-lig-coot-4.pdb"
Chain information for NTSR1-ARRB2 C1 model J4765_arrestin2-coot-1.pdb #1
---
Chain | Description
B | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
Chain information for NTSR1-ARRB2-N065 model -coot-9-2.pdb #2
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
Chain information for NTSR1-ARRB2-N191 model _R-lig-coot-4.pdb #3
---
Chain | Description
A | No description available
D | No description available
E | No description available
L | No description available
Q | No description available
> show cartoons
Computing secondary structure
[Repeated 2 time(s)]
> style stick
Changed 34157 atom styles
> hide target a
> ui tool show Matchmaker
>
Missing command
>
Missing command
> reset prefs
Unknown command: reset prefs
>
Missing command
>
Missing command
>
Missing command
>
Missing command
> help help:user/tools/matchmaker.html
>
Missing command
> toolshed install chimerax.matchmaker
chimerax.matchmaker does not match any bundles
> toolshed install matchmaker
ChimeraX-MatchMaker (2.1.6) is already installed
>
Missing command
>
Missing command
>
Missing command
>
Missing command
> toolshed list
List of installed bundles:
* AddCharge (1.5.18): Add partial charges to atoms
* AddH (2.2.6): Add hydrogens
* AlignmentAlgorithms (2.0.2): Sequence alignment algorithms
* AlignmentHdrs (3.5): Alignment header support
* AlignmentMatrices (2.1): Sequence alignment similarity matrices
* Alignments (2.16.1): Sequence alignment support
* AllMetal3D (0.8): AllMetal3D: Predict metal and water binding sites in proteins
* AlphaFold (1.0.1): Predict or fetch AlphaFold structures
* AltlocExplorer (1.1.2): Examine/change alternate atomic locations
* AmberInfo (1.0): Provide information about AmberTools installation
* Arrays (1.1): C++ library for parsing numpy arrays
* Atomic (1.58.8): Atomic-structure functionality
* AtomicLibrary (14.1.11): Atomic-structure C++ library
* AtomSearch (2.0.1): 3D atom search
* AxesPlanes (2.4): Depict axes or planes
* BasicActions (1.1.2): Basic actions for user-defined specifier names
* BILD (1.0): BILD file reader
* BlastProtein (3.0.0): Search PDB/NR/AlphaFold using BLAST
* BondRot (2.0.4): Bond rotation support
* BugReporter (1.0.1): Report bugs when an error occurs
* BuildStructure (2.13.1): Create/modify structures
* Bumps (1.0): Find protrusions in density maps
* ButtonPanel (1.0.1): Create custom user interface panels
* CageBuilder (1.0.1): Build polygonal meshes for oligomeric molecular assemblies
* CellPack (1.0): Fetch cellPACK models from web
* Centroids (1.4): Depict centroid of atoms
* ChangeChains (1.1): Change chain IDs
* CheckWaters (1.4): Check water placement in maps
* ChemGroup (2.0.1): Detect chemically functional groups
* Clashes (2.3): Find clashes/contacts in structures
* ColorActions (1.0.5): Simple interface for coloring objects
* ColorGlobe (1.0): Show directional resolution colored sphere
* ColorKey (1.5.6): Add color key to graphics
* CommandLine (1.2.5): Command line support
* ConnectStructure (2.0.1): Add bonds to structures that lack them
* Contacts (1.0.1): Display chain contact maps
* Core (1.9): ChimeraX Core Package
* CoreFormats (1.2): ChimeraX session support
* coulombic (1.4.4): Compute/show electrostatic potential
* Crosslinks (1.0): Analyze crosslinks
* Crystal (1.0): Crystal symmetries
* CrystalContacts (1.0.1): Show contacting asymmetric units in a crystal
* Cytoscape (0.1): Cytoscape interface
* DataFormats (1.2.3): Data format management
* Dicom (1.2.6): Read medical imaging and segmentations in DICOM format
* DistMonitor (1.4.2): Interactive distance display
* DockPrep (1.1.3): Prepare structures for docking
* Dssp (2.0): Compute/assign secondary structure
* EMDB-SFF (1.0): EMDB SFF file reader
* ESMFold (1.0): Predict or fetch ESMFold structures
* FileHistory (1.0.1): File History Panel
* FunctionKey (1.0.1): Assign function keys to run commands
* Geometry (1.3): Vector and coordinate system routines
* gltf (1.0): Read/write glTF 3d scene files
* Graphics (1.4.1): OpenGL graphics rendering
* Hbonds (2.5): Identify hydrogen bonds in and among structures
* Help (1.3): Show ChimeraX Help
* HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
* IHM (1.1): Integrative Hybrid Models file reader
* ImageFormats (1.2): Support for saving images
* IMOD (1.0): IMOD model file reader
* IO (1.0.3): Python convenience input/output functions
* ItemsInspection (1.0.1): Inspection of attributes of a set of items
* IUPAC (1.0): IUPAC fetch
* KVFinder (1.2.1): Find cavities/pockets
* Label (1.1.14): Add text labels to graphics
* LigandRecognizer (0.2): This tool uses a PDB model (.pdb or .cif) and corresponding density map (.cpp4) to validate/identify ligands.
* ListInfo (1.2.2): Report attributes for selected atomic data
* Log (1.2): Log support
* LookingGlass (1.1): LookingGlass holographic display
* Maestro (1.9.1): Maestro reader
* Map (1.3): Density maps
* MapData (2.0): Volume data file formats
* MapEraser (1.0.1): Map eraser
* MapFilter (2.0.1): Operations on maps
* MapFit (2.0): Fit molecules into maps
* MapSeries (2.1.1): Volume series
* Markers (1.0.1): Place markers on density maps
* Mask (1.0.2): Mask a volume to a surface
* MatchMaker (2.1.6): Superimpose structures
* MCopy (1.0): Copy atomic structure attributes to another structure
* MDcrds (2.7.2): Molecular dynamics support
* MedicalToolbar (1.1): Toolbar for medical image analysis
* Meeting (1.0.1): Shared interactive VR sessions.
* MLP (1.1.1): Molecular lipophilicity calculation
* mmCIF (2.14.2): mmCIF format read/write
* MMTF (2.2): MMTF format read/write
* ModelArchive (1.0): Fetch structures from Model Archive and display PAE plots
* Modeller (1.5.18): Interface to Modeller
* ModelPanel (1.5): ChimeraX Model Panel
* ModelSeries (1.0.1): Display sequences of models one by one
* Mol2 (2.0.3): Mol2 reader/writer
* Mole (1.0): Open JSON tunnel files from Mole
* MolecularDynamicsViewer (1.6): A UI tool for loading and viewing a multiframe pdb file
* Morph (1.0.2): Morph atomic structures
* MouseModes (1.2): Provide right button mouse mode tool
* Movie (1.0): Commands to record movies
* MutationScores (1.0): Visualize deep mutational scanning data
* Neuron (1.0): Read SWC neuron trace files
* Nifti (1.2): Read medical images in NIfTI format
* NIHPresets (1.2.7): NIH3D presets
* NMRSTAR (1.0.2): Read NMR distance restraints from NMR-STAR files
* NRRD (1.2): Read medical images in NRRD format
* Nucleotides (2.0.3): Create nucleotide-specific displays
* OpenCommand (1.14): Manages 'open' command extensibility
* OrthoPick (1.0.1): Show orthogonal views for tomogram particle picking
* PDB (2.7.6): PDB format read/write
* PDBBio (1.0.1): PDB biological assembly fetch
* PDBLibrary (1.0.4): C++ PDB support
* PDBMatrices (1.0): Crystal and biological unit matrices
* PickBlobs (1.0.1): Measure and color blobs
* Positions (1.0): Read and write model position matrices
* PresetMgr (1.1.2): Preset management
* PubChem (2.2): PubChem fetch
* ReadPbonds (1.0.1): Read in pseudobonds from a file
* Registration (1.1.2): Register ChimeraX
* RemoteControl (1.0): Control ChimeraX from other apps
* RenderByAttr (1.6.2): Depict attribute values on structures
* RenumberResidues (1.1): Renumber residues
* ResidueFit (1.0.1): Display fit of residues to density map
* RestServer (1.3.1): Starts REST server to execute commands from network requests
* RNALayout (1.0): Make RNA models
* RotamerLibMgr (4.0): Manage rotamer libraries
* RotamerLibsDunbrack (2.0): Dunbrack rotamer library
* RotamerLibsDynameomics (2.0): Dynameomics rotamer library
* RotamerLibsRichardson (2.0): Richardson rotamer libraries
* SaveCommand (1.5.1): Manages 'save' command extensibility
* SchemeMgr (1.0): HTTP scheme management
* SDF (2.0.2): SDF file reader
* Segger (1.0): Segment map
* Segment (1.0.1): Watershed segment calculation
* Segmentations (3.5.6): Segment any volume data
* SelInspector (1.0): Inspect contents of selection
* SeqView (2.14): Sequence viewer
* Shape (1.0.1): Make models for geometric shapes
* Shell (1.0.1): Interactive Python shell
* Shortcuts (1.2.0): Button and keyboard shortcuts
* ShowSequences (1.0.3): Choose/show structure sequences
* SideView (1.0.1): Side view of scene
* SimilarStructures (1.0.1): Visualize similar structures found using Foldseek, MMseqs2 or BLAST
* Smiles (2.1.2): SMILES fetch
* SmoothLines (1.0): Smooth network of lines
* SpaceNavigator (1.0): Space Navigator device support
* StdCommands (1.18.1): Standard commands
* STL (1.0.1): STL file read/write
* Storm (1.0): STORM file reader
* StructMeasure (1.2.1): Structure measurement user interface
* Struts (1.0.1): struts for 3D printing
* Surface (1.0.1): Surface calculations
* SwapAA (2.0.1): Swap amino acid
* SwapRes (2.5): Swap residue side chains
* TapeMeasure (1.0): Tape measure mouse mode
* TaskManager (1.0): Manage background tasks in ChimeraX
* Test (1.0): simple regression test
* Toolbar (1.2.3): Toolbar
* ToolshedUtils (1.2.4): Toolshed bundle utilities
* Topography (1.0): Show a topographic surface for a 2D image
* ToQuest (1.0): Copy scenes to VR Quest headset
* Tug (1.0.1): Tug on atoms with molecular dynamics
* UI (1.41): ChimeraX user interface
* Umap (1.0): Utilities for installing and using UMAP
* uniprot (2.3.1): UniProt database support
* UnitCell (1.0.1): Show crystal unit cell
* ViewDockX (1.4.4): Analyze ligand-receptor docking results
* VIPERdb (1.0): Read Virus Particle Explorer .vdb files
* Vive (1.1): Virtual reality headset support
* VolumeMenu (1.0.1): Volume menu
* vrml (1.0): Write basic VRML output for 3D color printing
* VTK (1.0): Legacy VTK file reader and writer
* WavefrontOBJ (1.0): Wavefront OBJ file read/write
* WebCam (1.0.2): Combine camera video with graphics
* WebServices (1.1.4): Web service and HTTP request support
* Zone (1.0.1): Mouse mode to show atom and map zones
> enable ChimeraX-MatchMaker
Unknown command: toolshed enable ChimeraX-MatchMaker
> usage matchmaker
> help matchmaker
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/help_viewer/cmd.py", line 81, in help
url = cli.command_url(cmd_name)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3350, in command_url
return _get_help_url(cmd.command_name.split())
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'split'
AttributeError: 'NoneType' object has no attribute 'split'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3350, in command_url
return _get_help_url(cmd.command_name.split())
^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AV001QNZP/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 7天7小时11分钟
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 27E1N5900:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AllMetal3D: 0.8
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-Cytoscape: 0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.2.7
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
fsspec: 2025.3.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
gradio_client: 0.11.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
huggingface-hub: 0.29.3
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
PyYAML: 6.0.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
tqdm: 4.67.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
websockets: 11.0.3
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (1)
comment:1 by , 8 months ago
| Component: | Unassigned → Tool Shed |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ChimeraX forgets matchmaker command after installing other bundles |
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