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Opened 22 months ago
Closed 22 months ago
#14413 closed defect (can't reproduce)
Region not in regions list
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/question2.cxs"
Log from Fri Jan 19 01:10:23 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/1dzo_coord (2).pdb"
> "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN 588
> Computational protein design/Lab2/pilin_ID.pdb"
Chain information for 1dzo_coord (2).pdb #1
---
Chain | Description
A | No description available
Chain information for pilin_ID.pdb #2
---
Chain | Description
A | No description available
> preset publication 1
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> hide #1 models
> hide #2 models
> show #2 models
> show #1 models
> color #2 #aa7942ff
> color #2 #ff9300ff
> color #2 white
> color #2 #fffb00ff
> color #2 #ff40ffff
> color #2 #00f900ff
> hide #1 models
> color #1 #00f900ff
> show #1 models
> ui tool show Matchmaker
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1dzo_coord (2).pdb, chain A (#1) with pilin_ID.pdb, chain A (#2),
sequence alignment score = 610.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 1dzo_coord (2).pdb #1/A,
pilin_ID.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 120 pruned atom pairs is 0.000 angstroms; (across all 120 pairs:
0.000)
> open "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/design3_pilin_ID.pdb"
Summary of feedback from opening /Users/jihun/Library/CloudStorage/OneDrive-
UW/2023 Lecture-UW/BIOEN 588 Computational protein
design/Lab2/design3_pilin_ID.pdb
---
warnings | Ignored bad PDB record found on line 1725
Ignored bad PDB record found on line 1726
complete: res ss phi psi omega frag rama seq
Ignored bad PDB record found on line 1727
1 L 0.000 0.000 0.000 ---- 0.00 G
Ignored bad PDB record found on line 1728
2 L 0.000 0.000 0.000 ---- 0.00 T
Ignored bad PDB record found on line 1729
3 L 0.000 0.000 0.000 ---- 0.00 E
117 messages similar to the above omitted
Chain information for design3_pilin_ID.pdb #3
---
Chain | Description
A | No description available
Associated design3_pilin_ID.pdb chain A to pilin_ID.pdb, chain A with 3
mismatches
Chains used in RMSD evaluation for alignment 1: 1dzo_coord (2).pdb #1/A,
pilin_ID.pdb #2/A, design3_pilin_ID.pdb #3/A
> hide #2 models
> ui tool show Matchmaker
> matchmaker #3 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1dzo_coord (2).pdb, chain A (#1) with design3_pilin_ID.pdb, chain A
(#3), sequence alignment score = 596.8
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 1dzo_coord (2).pdb #1/A,
design3_pilin_ID.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 120 pruned atom pairs is 0.000 angstroms; (across all 120 pairs:
0.000)
> select #2/A:28,66,126 #3/A:4,42,102
82 atoms, 77 bonds, 6 residues, 2 models selected
> select #1/A #2/A #3/A
4240 atoms, 4275 bonds, 360 residues, 3 models selected
> select #1:4
Nothing selected
> select #1/A1
Nothing selected
> select #1/A2
Nothing selected
> select #1/A.1
Expected an objects specifier or a keyword
> select #1/A 117
Expected a keyword
> select #1/A.117
Expected an objects specifier or a keyword
> select #1/A117
Nothing selected
> select #1/A1
Nothing selected
> select #1/A:1
Nothing selected
> select #1:1
Nothing selected
> select :1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select :4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1:4
Nothing selected
> select #3:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1:4
Nothing selected
> select #1:4
Nothing selected
> select add #3:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1:102
18 atoms, 17 bonds, 2 residues, 2 models selected
> select add #3:102
29 atoms, 27 bonds, 3 residues, 2 models selected
> select #1/A:102 #3/A:4,102
29 atoms, 27 bonds, 3 residues, 2 models selected
> select #1/A:102 #3/A:4,102
29 atoms, 27 bonds, 3 residues, 2 models selected
> style sel stick
Changed 29 atom styles
> show #2 models
> hide #2 models
> style sel ball
Changed 29 atom styles
> style sel stick
Changed 29 atom styles
> color sel cyan
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> undo
[Repeated 9 time(s)]
> color green
> select #1:4
Nothing selected
> select #3:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1:28
18 atoms, 17 bonds, 2 residues, 2 models selected
> select add #3:102
29 atoms, 27 bonds, 3 residues, 2 models selected
> select add #1:126
37 atoms, 34 bonds, 4 residues, 2 models selected
> style sel stick
Changed 37 atom styles
> show sel target ab
> color sel byhetero
> hide #1 models
> show #1 models
> select sel @< 4
281 atoms, 254 bonds, 42 residues, 3 models selected
> select sel @< 4
695 atoms, 629 bonds, 100 residues, 3 models selected
> color (#1,3 & sel) cyan
> select clear
> select #3:4
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1:126
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #1:126
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #3:102
26 atoms, 23 bonds, 3 residues, 2 models selected
> select add #1:28
37 atoms, 34 bonds, 4 residues, 2 models selected
> color sel magenta
> color sel byhetero
> select clear
> hide #3 models
> hide #1 models
> show #3 models
> show #1 models
> select clear
[Repeated 3 time(s)]
> hide #3 models
> show #3 models
> save "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/question1.cxs"
> hide #1 models
> hide #3 models
> open "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/pilin_AFD.pdb"
Summary of feedback from opening /Users/jihun/Library/CloudStorage/OneDrive-
UW/2023 Lecture-UW/BIOEN 588 Computational protein design/Lab2/pilin_AFD.pdb
---
warnings | Ignored bad PDB record found on line 1741
Ignored bad PDB record found on line 1742
complete: res ss phi psi omega frag rama seq
Ignored bad PDB record found on line 1743
1 L 0.000 0.000 0.000 ---- 0.00 G
Ignored bad PDB record found on line 1744
2 L 0.000 0.000 0.000 ---- 0.00 T
Ignored bad PDB record found on line 1745
3 L 0.000 0.000 0.000 ---- 0.00 E
117 messages similar to the above omitted
Chain information for pilin_AFD.pdb #4
---
Chain | Description
A | No description available
Associated pilin_AFD.pdb chain A to 1dzo_coord (2).pdb, chain A with 0
mismatches
Chains used in RMSD evaluation for alignment 2: 1dzo_coord (2).pdb #1/A,
design3_pilin_ID.pdb #3/A, pilin_AFD.pdb #4/A
> show #1 models
> hide #1 models
> color green
> ui tool show Matchmaker
> matchmaker #4 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1dzo_coord (2).pdb, chain A (#1) with pilin_AFD.pdb, chain A (#4),
sequence alignment score = 610.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 1dzo_coord (2).pdb #1/A,
pilin_AFD.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 120 pruned atom pairs is 0.000 angstroms; (across all 120 pairs:
0.000)
> select #1/A #4/A #3/A
4308 atoms, 4343 bonds, 360 residues, 3 models selected
> color byattribute
Missing or invalid "attrName" argument: Expected a text string
> seq_conservation palette magenta:cyan.
Unknown command: seq_conservation palette magenta:cyan.
> save "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/question2.cxs"
> color byattribute seq_conservation
5979 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> undo
> color byattribute
Missing or invalid "attrName" argument: Expected a text string
> seq_conservation palette magenta:cyan
Unknown command: seq_conservation palette magenta:cyan
> color byattribute seq_conservation palette magenta:cyan
5979 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> show #1 models
> show #2 models
> show #3 models
> hide #3 models
> hide #2 models
> show #3 models
> show #2 models
> hide #1 models
> hide #2 models
> hide #3 models
> show #1 models
> hide #4 models
> delete #4
> open "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/design1_pilin_AFD.pdb"
Summary of feedback from opening /Users/jihun/Library/CloudStorage/OneDrive-
UW/2023 Lecture-UW/BIOEN 588 Computational protein
design/Lab2/design1_pilin_AFD.pdb
---
warnings | Ignored bad PDB record found on line 1741
Ignored bad PDB record found on line 1742
complete: res ss phi psi omega frag rama seq
Ignored bad PDB record found on line 1743
1 L 0.000 0.000 0.000 ---- 0.00 G
Ignored bad PDB record found on line 1744
2 L 0.000 0.000 0.000 ---- 0.00 T
Ignored bad PDB record found on line 1745
3 L 0.000 0.000 0.000 ---- 0.00 E
117 messages similar to the above omitted
Chain information for design1_pilin_AFD.pdb #4
---
Chain | Description
A | No description available
Associated design1_pilin_AFD.pdb chain A to pilin_AFD.pdb, chain A with 0
mismatches
Chains used in RMSD evaluation for alignment 1: 1dzo_coord (2).pdb #1/A,
design1_pilin_AFD.pdb #4/A
> color green
> save "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/question2.cxs"
——— End of log from Fri Jan 19 01:10:23 2024 ———
opened ChimeraX session
> color byattribute seq_conservation palette magenta:cyan
5979 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> delete #1
> open "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/1dzo_coord (2).pdb"
Chain information for 1dzo_coord (2).pdb #1
---
Chain | Description
A | No description available
Associated 1dzo_coord (2).pdb chain A to pilin_AFD.pdb, chain A with 0
mismatches
> color byattribute seq_conservation palette magenta:cyan
5979 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> select subtract #3
Nothing selected
> select add #4
1739 atoms, 1751 bonds, 120 residues, 1 model selected
> select add #2
3410 atoms, 3434 bonds, 240 residues, 2 models selected
> select subtract #2
1739 atoms, 1751 bonds, 120 residues, 1 model selected
> select add #1
2585 atoms, 2609 bonds, 240 residues, 2 models selected
> color byattribute seq_conservation palette magenta:cyan
5979 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> hide #4 models
> hide #1 models
> show #4 models
> hide #4 models
> show #4 models
> show #1 models
> color byattribute seq_conservation palette magenta:cyan
5979 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> show #2 models
> show #3 models
> hide #2 models
> hide #3 models
> ui tool show Matchmaker
> matchmaker #4 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1dzo_coord (2).pdb, chain A (#1) with design1_pilin_AFD.pdb, chain
A (#4), sequence alignment score = 610.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 1dzo_coord (2).pdb #1/A,
design1_pilin_AFD.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 120 pruned atom pairs is 0.000 angstroms; (across all 120 pairs:
0.000)
> open "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/design1_pilin_AFD.pdb"
Summary of feedback from opening /Users/jihun/Library/CloudStorage/OneDrive-
UW/2023 Lecture-UW/BIOEN 588 Computational protein
design/Lab2/design1_pilin_AFD.pdb
---
warnings | Ignored bad PDB record found on line 1800
Ignored bad PDB record found on line 1801
complete: res ss phi psi omega frag rama seq
Ignored bad PDB record found on line 1802
1 L 0.000 0.000 0.000 ---- 0.00 G
Ignored bad PDB record found on line 1803
2 L 0.000 0.000 0.000 ---- 0.00 T
Ignored bad PDB record found on line 1804
3 L 0.000 0.000 0.000 ---- 0.00 E
117 messages similar to the above omitted
Chain information for design1_pilin_AFD.pdb #5
---
Chain | Description
A | No description available
> hide #4 models
> select add #5
4383 atoms, 4418 bonds, 360 residues, 3 models selected
> select subtract #4
2644 atoms, 2667 bonds, 240 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #5 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1dzo_coord (2).pdb, chain A (#1) with design1_pilin_AFD.pdb, chain
A (#5), sequence alignment score = 513.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 1dzo_coord (2).pdb #1/A,
design1_pilin_AFD.pdb #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 120 pruned atom pairs is 0.000 angstroms; (across all 120 pairs:
0.000)
> delete #4
> color byattribute seq_conservation palette magenta:cyan
6038 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> color byattribute seq_conservation palette yellow:cyan
6038 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> color byattribute seq_conservation magenta:cyan
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute seq_conservation cyan
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute seq_conservation palette cyan-gray-maroon
6038 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> color byattribute seq_conservation cyan
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
Could not find palette magenta at COLOURlovers.com using keyword search
Could not find palette magenta at COLOURlovers.com using keyword search
> color byattribute seq_conservation palette magenta:cyan
6038 atoms, 480 residues, atom seq_conservation range -6.22 to 1
> select clear
> select #1/A:109
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select clear
> select #1/A:81
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/A:110
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #1/A:109
22 atoms, 20 bonds, 3 residues, 1 model selected
> select add #5
1820 atoms, 1829 bonds, 123 residues, 2 models selected
> select clear
> select add #1/A:109
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A #5/A
2644 atoms, 2667 bonds, 240 residues, 2 models selected
> select clear
> select #1/A #5/A
2644 atoms, 2667 bonds, 240 residues, 2 models selected
> ui dockable false "Sequence Viewer"
> ui dockable true "Sequence Viewer"
> select clear
> select add #1/A:31
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/A:35
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #1/A:34
17 atoms, 14 bonds, 3 residues, 1 model selected
> select subtract #1/A:34
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #1/A:34
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #1/A:33
21 atoms, 17 bonds, 4 residues, 1 model selected
> select add #1/A:109
28 atoms, 24 bonds, 5 residues, 1 model selected
> select add #1/A:110
34 atoms, 29 bonds, 6 residues, 1 model selected
> select add #1/A:81
43 atoms, 37 bonds, 7 residues, 1 model selected
> select add #1/A:139
50 atoms, 44 bonds, 8 residues, 1 model selected
> select add #1/A:140
59 atoms, 52 bonds, 9 residues, 1 model selected
> select add #1/A:45
66 atoms, 58 bonds, 10 residues, 1 model selected
> select add #1/A:44
75 atoms, 66 bonds, 11 residues, 1 model selected
> select add #1/A:126
83 atoms, 73 bonds, 12 residues, 1 model selected
> select add #1/A:124
91 atoms, 80 bonds, 13 residues, 1 model selected
> select add #1/A:123
96 atoms, 84 bonds, 14 residues, 1 model selected
> select add #1/A:122
101 atoms, 88 bonds, 15 residues, 1 model selected
> select add #1/A:121
108 atoms, 94 bonds, 16 residues, 1 model selected
> select add #1/A:99
115 atoms, 100 bonds, 17 residues, 1 model selected
> select add #1/A:88
121 atoms, 105 bonds, 18 residues, 1 model selected
> select add #1/A:101
128 atoms, 111 bonds, 19 residues, 1 model selected
> select add #1/A:86
133 atoms, 115 bonds, 20 residues, 1 model selected
> select add #1/A:75
140 atoms, 121 bonds, 21 residues, 1 model selected
> select add #1/A:67
147 atoms, 127 bonds, 22 residues, 1 model selected
> select add #1/A:63
154 atoms, 133 bonds, 23 residues, 1 model selected
> select add #1/A:115
162 atoms, 140 bonds, 24 residues, 1 model selected
> select add #1/A:134
170 atoms, 147 bonds, 25 residues, 1 model selected
> color sel magenta
> select add #1/A:38
175 atoms, 151 bonds, 26 residues, 1 model selected
> select add #1/A:96
180 atoms, 155 bonds, 27 residues, 1 model selected
Drag select of 2 residues
> color sel magenta
> select add #1/A:96
28 atoms, 4 bonds, 3 residues, 2 models selected
> select add #1/A:38
33 atoms, 8 bonds, 4 residues, 2 models selected
> color sel magenta
> show sel atoms
[Repeated 1 time(s)]Drag select of 19 atoms, 240 residues, 15 bonds
Drag select of 2 atoms, 106 residues, 1 bonds
Drag select of 19 atoms, 240 residues, 15 bonds
> select clear
Drag select of 19 atoms, 240 residues, 15 bonds
> show sel atoms
> hide hydrogen
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Fetching compressed palette cyans from
https://www.colourlovers.com/api/palettes?keywords=cyans&format=json&numResults=100
Could not find palette cyans at COLOURlovers.com using keyword search
> select hydrogen
Expected an objects specifier or a keyword
> select hydrogens
Expected an objects specifier or a keyword
> select clear
> hide #1 models
> hide #5 models
> show #5 models
> show #1 models
> hide #5 models
> color #1 byhetero
> hide #1 models
> show #5 models
> select add #5/A:21
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #5/A:14
31 atoms, 29 bonds, 2 residues, 1 model selected
> select add #5/A:77
48 atoms, 45 bonds, 3 residues, 1 model selected
> select add #5/A:19@1HB
49 atoms, 45 bonds, 4 residues, 1 model selected
> select subtract #5/A:19
48 atoms, 45 bonds, 3 residues, 1 model selected
Drag select of 5 atoms, 1 residues, 2 bonds
> select subtract #5/A:51
55 atoms, 47 bonds, 4 residues, 1 model selected
> select add #5/A:51
74 atoms, 65 bonds, 5 residues, 1 model selected
> select add #5/A:57
85 atoms, 75 bonds, 6 residues, 1 model selected
> select add #5/A:11
107 atoms, 96 bonds, 7 residues, 1 model selected
> select add #5/A:7
122 atoms, 110 bonds, 8 residues, 1 model selected
> select add #5/A:10
137 atoms, 124 bonds, 9 residues, 1 model selected
> select add #5/A:20
161 atoms, 147 bonds, 10 residues, 1 model selected
> select add #5/A:102
178 atoms, 163 bonds, 11 residues, 1 model selected
> select add #5/A:75
200 atoms, 184 bonds, 12 residues, 1 model selected
> select add #5/A:62
222 atoms, 205 bonds, 13 residues, 1 model selected
> select add #5/A:85
244 atoms, 226 bonds, 14 residues, 1 model selected
> select add #5/A:86
263 atoms, 244 bonds, 15 residues, 1 model selected
> select add #5/A:110
278 atoms, 258 bonds, 16 residues, 1 model selected
> select add #5/A:115
288 atoms, 267 bonds, 17 residues, 1 model selected
> select add #5/A:97
307 atoms, 285 bonds, 18 residues, 1 model selected
> select add #5/A:98
324 atoms, 302 bonds, 19 residues, 1 model selected
> select add #5/A:100
338 atoms, 315 bonds, 20 residues, 1 model selected
> select add #5/A:72
349 atoms, 325 bonds, 21 residues, 1 model selected
> select add #5/A:43
371 atoms, 346 bonds, 22 residues, 1 model selected
> select add #5/A:39
382 atoms, 356 bonds, 23 residues, 1 model selected
> select subtract #5/A:98
365 atoms, 339 bonds, 22 residues, 1 model selected
> select add #5/A:98
382 atoms, 356 bonds, 23 residues, 1 model selected
> color sel magenta
> select clear
> select add #5/A:64
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #5/A:91
31 atoms, 30 bonds, 2 residues, 1 model selected
> select add #5/A:116
46 atoms, 44 bonds, 3 residues, 1 model selected
> select add #5/A:99@CB
47 atoms, 44 bonds, 4 residues, 1 model selected
> color sel magenta
> select add #5/A:9
57 atoms, 53 bonds, 5 residues, 1 model selected
> select add #5/A:99@CG
58 atoms, 55 bonds, 5 residues, 1 model selected
> select add #5/A:99@2HG
59 atoms, 59 bonds, 5 residues, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> select #5/A:99
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
Drag select of 1177 atoms, 120 residues, 1082 bonds
> color sel byhetero
[Repeated 1 time(s)]
> select clear
> select add #5
1798 atoms, 1809 bonds, 120 residues, 1 model selected
> color sel byhetero
> hide sel target a
> undo
> select clear
> select H
2581 atoms, 360 residues, 3 models selected
> hide (#5 & sel) target a
> select clear
> save "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/question2.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot
'region browser': self.region_manager.state(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^
ValueError: <chimerax.seq_view.region_browser.Region object at 0x295845210> is
not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16df13650> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x291786110>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at 0x291786110>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at
0x291786110>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot
'region browser': self.region_manager.state(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^
ValueError: <chimerax.seq_view.region_browser.Region object at 0x295845210> is
not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16df13650> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x291786110>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at 0x291786110>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at
0x291786110>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/question2_2.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot
'region browser': self.region_manager.state(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^
ValueError: <chimerax.seq_view.region_browser.Region object at 0x295845210> is
not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16df13650> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x291786110>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at 0x291786110>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at
0x291786110>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot
'region browser': self.region_manager.state(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^
ValueError: <chimerax.seq_view.region_browser.Region object at 0x295845210> is
not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16df13650> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x291786110>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at 0x291786110>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at
0x291786110>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> show #1 models
> hide #5 models
> hide #1 models
> show #5 models
> select #1/A #5/A
2644 atoms, 2667 bonds, 240 residues, 2 models selected
> select clear
> show #1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> select clear
> hide #1 models
> show #1 models
> hide #5 models
> hide #1 models
> show #5 models
> delete #2
> delete E3
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #3
> save "/Users/jihun/Library/CloudStorage/OneDrive-UW/2023 Lecture-UW/BIOEN
> 588 Computational protein design/Lab2/question2_2.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot
'region browser': self.region_manager.state(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^
ValueError: <chimerax.seq_view.region_browser.Region object at 0x295845210> is
not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16df13650> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x291786110>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at 0x291786110>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at
0x291786110>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot
'region browser': self.region_manager.state(),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
^^^^^^^^^^^^^^^^^^^^^
ValueError: <chimerax.seq_view.region_browser.Region object at 0x295845210> is
not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16df13650> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x291786110>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at 0x291786110>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16df13650> -> <chimerax.seq_view.tool.SequenceViewer object at
0x291786110>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63KH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 1 hour, 54 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (3)
comment:1 by , 22 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Region not in regions list |
comment:2 by , 22 months ago
comment:3 by , 22 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Hi Jihun,
Thanks for reporting this problem. I tried a few things but could not reproduce it myself. It's possible that if you provided the session/PDB files you were using that I might be able to reproduce it, but it's not guaranteed and whether you want to share those files is completely up to you.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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Reported by Jihun Jeung