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Opened 22 months ago
Closed 22 months ago
#14489 closed defect (can't reproduce)
MatchMaker: IndexError: vector
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fidel.lozano@fhnw.ch/Library/CloudStorage/OneDrive-
> FHNW/PROJECTS/02_NanoParticles/Peptide_design/polyA_modeling.cxs
Log from Fri Jan 26 10:24:23 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fidel.lozano@fhnw.ch/Library/CloudStorage/OneDrive-
> FHNW/PROJECTS/02_NanoParticles/Peptide_design/polyA_modeling.cxs
Log from Thu Apr 27 15:03:48 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fidel.lozano@fhnw.ch/Library/CloudStorage/OneDrive-
> FHNW/Peptides-NanoParticles/peptide_design/polyA_modeling.cxs
Log from Mon Apr 3 11:47:31 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/fidel.lozano@fhnw.ch/Desktop/peptides_polyA.cxs
Log from Fri Mar 31 17:43:09 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show "Build Structure"
Populating font family aliases took 65 ms. Replace uses of missing font family
"Calibri" with one that exists to avoid this cost.
> build start peptide polyA_full YAKAQAKAAKAQAKAAKAQAKAQAKAR -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack
Chain information for polyA_full #1
---
Chain | Description
A | No description available
> show atoms
> save /Users/fidel.lozano@fhnw.ch/Desktop/polyApeptide.pdb relModel #1
> open /Users/fidel.lozano@fhnw.ch/Desktop/peptide1_polyA.pdb
Chain information for peptide1_polyA.pdb #2
---
Chain | Description
A | No description available
> open /Users/fidel.lozano@fhnw.ch/Desktop/peptide1_polyA.pdb
Chain information for peptide1_polyA.pdb #3
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2 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 polyA_full, chain A (#1) with peptide1_polyA.pdb, chain A (#2),
sequence alignment score = 126.3
RMSD between 27 pruned atom pairs is 0.000 angstroms; (across all 27 pairs:
0.000)
> select add #2
215 atoms, 215 bonds, 31 residues, 1 model selected
> show sel atoms
> ui tool show Matchmaker
> matchmaker #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 polyA_full, chain A (#1) with peptide1_polyA.pdb, chain A (#3),
sequence alignment score = 126.3
RMSD between 27 pruned atom pairs is 0.000 angstroms; (across all 27 pairs:
0.000)
> select subtract #2
Nothing selected
> hide #2 models
> hide #1 models
> show #2 models
> show #1 models
> save /Users/fidel.lozano@fhnw.ch/Desktop/peptides_polyA.cxs
\u2014\u2014\u2014 End of log from Fri Mar 31 17:43:09 2023 \u2014\u2014\u2014
opened ChimeraX session
> hide #2 models
> show #2 models
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> hide #3 models
> show #3 models
> rename #2 polyA_2.pdb
> rename #3 polyA_3.pdb
> hide #2 models
> hide #3 models
> hide #1 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> select add #2/A:15
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/A:17
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #2/A:16
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add #2/A:18
24 atoms, 20 bonds, 4 residues, 1 model selected
> select add #2/A:20
29 atoms, 24 bonds, 5 residues, 1 model selected
> select add #2/A:19
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add #2/A:21
47 atoms, 40 bonds, 7 residues, 1 model selected
> select add #2/A:22
52 atoms, 44 bonds, 8 residues, 1 model selected
> select add #2/A:23
61 atoms, 52 bonds, 9 residues, 1 model selected
> select add #2/A:24
66 atoms, 56 bonds, 10 residues, 1 model selected
> select add #2/A:25
75 atoms, 64 bonds, 11 residues, 1 model selected
> select add #2/A:26
80 atoms, 68 bonds, 12 residues, 1 model selected
> select add #2/A:27
85 atoms, 72 bonds, 13 residues, 1 model selected
> select add #2/A:28
94 atoms, 80 bonds, 14 residues, 1 model selected
> select add #2/A:29
99 atoms, 84 bonds, 15 residues, 1 model selected
> select add #2/A:30
108 atoms, 92 bonds, 16 residues, 1 model selected
> select add #2/A:31
114 atoms, 97 bonds, 17 residues, 1 model selected
> delete sel
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> hide #2 models
> show #2 models
> show #1 models
> undo
[Repeated 1 time(s)]
> show #1 models
> show #2 models
> open /Users/fidel.lozano@fhnw.ch/Desktop/peptide1_polyA.pdb
Chain information for peptide1_polyA.pdb #4
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #4 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 polyA_full, chain A (#1) with peptide1_polyA.pdb, chain A (#4),
sequence alignment score = 126.3
RMSD between 27 pruned atom pairs is 0.000 angstroms; (across all 27 pairs:
0.000)
> select add #4
215 atoms, 215 bonds, 31 residues, 1 model selected
> show sel atoms
> select subtract #4
Nothing selected
> hide #2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select add #2
101 atoms, 101 bonds, 14 residues, 1 model selected
> delete sel
> rename #4 polyA_2.pdb
> select #1/A:16
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select add #1
193 atoms, 193 bonds, 27 residues, 1 model selected
> select subtract #1
Nothing selected
> select #4/A:16
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #4/A:17
14 atoms, 12 bonds, 2 residues, 1 model selected
> select subtract #4/A:17
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #4/A:17
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #4/A:19
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #4/A:18
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #4/A:20
33 atoms, 28 bonds, 5 residues, 1 model selected
> select add #4/A:21
42 atoms, 36 bonds, 6 residues, 1 model selected
> select add #4/A:22
47 atoms, 40 bonds, 7 residues, 1 model selected
> select add #4/A:23
56 atoms, 48 bonds, 8 residues, 1 model selected
> select add #4/A:25
65 atoms, 57 bonds, 9 residues, 1 model selected
> select add #4/A:24
70 atoms, 60 bonds, 10 residues, 1 model selected
> select add #4/A:26
75 atoms, 64 bonds, 11 residues, 1 model selected
> select add #4/A:27
80 atoms, 68 bonds, 12 residues, 1 model selected
> select add #4/A:28
89 atoms, 76 bonds, 13 residues, 1 model selected
> select add #4/A:30
98 atoms, 84 bonds, 14 residues, 1 model selected
> select add #4/A:29
103 atoms, 88 bonds, 15 residues, 1 model selected
> select add #4/A:31
109 atoms, 93 bonds, 16 residues, 1 model selected
> delete sel
> show #1 models
> show #3 models
> hide #4 models
> hide #1 models
> hide #3 models
> show #3 models
> select #3/A:9
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #3/A:10
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #3/A:12
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #3/A:11
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #3/A:13
33 atoms, 28 bonds, 5 residues, 1 model selected
> select add #3/A:14
42 atoms, 36 bonds, 6 residues, 1 model selected
> select add #3/A:15
47 atoms, 40 bonds, 7 residues, 1 model selected
> select add #3/A:16
52 atoms, 44 bonds, 8 residues, 1 model selected
> select add #3/A:17
61 atoms, 52 bonds, 9 residues, 1 model selected
> select add #3/A:18
66 atoms, 56 bonds, 10 residues, 1 model selected
> select add #3/A:19
75 atoms, 64 bonds, 11 residues, 1 model selected
> select add #3/A:20
80 atoms, 68 bonds, 12 residues, 1 model selected
> select add #3/A:21
89 atoms, 76 bonds, 13 residues, 1 model selected
> select add #3/A:22
94 atoms, 80 bonds, 14 residues, 1 model selected
> select add #3/A:23
103 atoms, 88 bonds, 15 residues, 1 model selected
> select add #3/A:24
108 atoms, 92 bonds, 16 residues, 1 model selected
> select add #3/A:25
117 atoms, 100 bonds, 17 residues, 1 model selected
> select add #3/A:26
122 atoms, 104 bonds, 18 residues, 1 model selected
> select add #3/A:27
127 atoms, 108 bonds, 19 residues, 1 model selected
> select add #3/A:28
136 atoms, 116 bonds, 20 residues, 1 model selected
> select add #3/A:29
141 atoms, 120 bonds, 21 residues, 1 model selected
> select add #3/A:30
150 atoms, 128 bonds, 22 residues, 1 model selected
> select add #3/A:31
156 atoms, 133 bonds, 23 residues, 1 model selected
> delete sel
> select add #3
59 atoms, 59 bonds, 8 residues, 1 model selected
> show sel atoms
> show #1 models
> show #4 models
> select clear
> hide #3 models
> hide #4 models
> select #1/A:3@NZ
1 atom, 1 residue, 1 model selected
> select add #1/A:7@NZ
2 atoms, 2 residues, 1 model selected
> ui mousemode right distance
> select #1/A:3@NZ
1 atom, 1 residue, 1 model selected
> select clear
> distance #1/A:7@NZ #1/A:3@NZ
Distance between polyA_full #1/A LYS 7 NZ and LYS 3 NZ: 8.181Å
> distance #1/A:3@NZ #1/A:10@NZ
Distance between polyA_full #1/A LYS 3 NZ and LYS 10 NZ: 11.000Å
> distance #1/A:3@NZ #1/A:21@NZ
Distance between polyA_full #1/A LYS 3 NZ and LYS 21 NZ: 27.355Å
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save /Users/fidel.lozano@fhnw.ch/Desktop/image5.png supersample 3
> select add #1
193 atoms, 193 bonds, 3 pseudobonds, 27 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "polyA_full_A SES surface": minimum -22.69, mean
-3.449, maximum 19.13
To also show corresponding color key, enter the above mlp command and add key
true
> color #1.1 #7b68eec3
> color #1.1 #7b68eebe
> mlp sel
Map values for surface "polyA_full_A SES surface": minimum -22.69, mean
-3.449, maximum 19.13
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> hide #1.1 models
> save /Users/fidel.lozano@fhnw.ch/Desktop/image6.png supersample 3
> show #1.1 models
> save /Users/fidel.lozano@fhnw.ch/Desktop/image7.png supersample 3
> hide #1.1 models
> show #3 models
> hide #3 models
> show #4 models
> hide #!1 models
> save /Users/fidel.lozano@fhnw.ch/Desktop/image8.png supersample 3
> show #3 models
> hide #4 models
> save /Users/fidel.lozano@fhnw.ch/Desktop/image9.png supersample 3
> save /Users/fidel.lozano@fhnw.ch/Desktop/peptides_polyA.cxs
\u2014\u2014\u2014 End of log from Mon Apr 3 11:47:31 2023 \u2014\u2014\u2014
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #3 models
> hide #2.1 models
> select add #1
193 atoms, 193 bonds, 3 pseudobonds, 27 residues, 2 models selected
> select subtract #1
1 model selected
> ui tool show "Build Structure"
Populating font family aliases took 51 ms. Replace uses of missing font family
"Calibri" with one that exists to avoid this cost.
> build start peptide "custom built" YAKAQAKAAKAQAKAA -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack
Chain information for custom built #5
---
Chain | Description
A | No description available
> hide #!1 models
> select add #5
112 atoms, 112 bonds, 16 residues, 1 model selected
> open /Users/fidel.lozano@fhnw.ch/Desktop/supercoil_peptide.pdb
Chain information for supercoil_peptide.pdb #6
---
Chain | Description
A | No description available
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
26 atoms, 25 bonds, 1 residue, 1 model selected
> select up
164 atoms, 163 bonds, 10 residues, 1 model selected
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> select clear
> select #5/A:4
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 14 residues, 1 model selected
> select up
112 atoms, 112 bonds, 16 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select clear
> select #5/A:16@O
1 atom, 1 residue, 1 model selected
> build join peptide sel length 1.33 omega 180 phi -120 move C
No carbons in specified atoms
> build join peptide sel length 1.33 omega 180 phi -120 move large
No carbons in specified atoms
> select clear
> select #5/A:16@C
1 atom, 1 residue, 1 model selected
> select add #6/A:1@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move large
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
10 atoms, 9 bonds, 2 residues, 1 model selected
> select up
262 atoms, 261 bonds, 25 residues, 1 model selected
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select add #5/A:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 14 residues, 1 model selected
> select up
274 atoms, 274 bonds, 26 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel atoms
> show sel cartoons
> rename #5 Half_coil
> color sel orange red
> color sel byhetero
> hide sel atoms
> color sel orange
> select clear
> select add #5
274 atoms, 274 bonds, 26 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui tool show "Basic Actions"
> ui tool show "Add Hydrogens"
> ~hbonds
[Repeated 1 time(s)]
> view sel
> hide sel target a
> show sel atoms
> undo
[Repeated 9 time(s)]
> select clear
Drag select of 62 atoms, 4 residues, 57 bonds
Drag select of 4 atoms, 3 residues, 2 bonds
> select clear
> select #5/A:21
21 atoms, 20 bonds, 1 residue, 1 model selected
> select up
168 atoms, 167 bonds, 11 residues, 1 model selected
> delete sel
> open /Users/fidel.lozano@fhnw.ch/Desktop/supercoil_peptide.pdb
Chain information for supercoil_peptide.pdb #6
---
Chain | Description
A | No description available
> select add #5/A:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 14 residues, 1 model selected
> hide sel cartoons
> color sel cyan
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 14 residues, 1 model selected
> select up
106 atoms, 106 bonds, 15 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> color sel light sea green
> color sel byhetero
> hide sel cartoons
> select clear
> select #5/A:15@O
1 atom, 1 residue, 1 model selected
> select add #6/A:1@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move large
No carbons in specified atoms
> select subtract #5/A:15@O
1 atom, 1 residue, 1 model selected
> select add #5/A:15@C
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move large
> undo
Undo failed, probably because structures have been modified.
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 183 atoms, 183 bonds
> ui tool show Matchmaker
> matchmaker #6 to #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match
score, s1, s2 = align(session, rseq, mseq,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align
score, seqs = NeedlemanWunsch.nw(ref, match,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in nw
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in
<listcomp>
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type
r = self.residue_at(loc)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
IndexError: vector
IndexError: vector
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
See log for complete Python traceback.
> matchmaker #6 to #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match
score, s1, s2 = align(session, rseq, mseq,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align
score, seqs = NeedlemanWunsch.nw(ref, match,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in nw
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in
<listcomp>
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type
r = self.residue_at(loc)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
IndexError: vector
IndexError: vector
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
See log for complete Python traceback.
> matchmaker #6 to #1/A pairing bs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 335, in match
score, s1, s2 = align(session, ref, seq, matrix, alg,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align
score, seqs = NeedlemanWunsch.nw(ref, match,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in nw
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in
<listcomp>
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type
r = self.residue_at(loc)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
IndexError: vector
IndexError: vector
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
See log for complete Python traceback.
> matchmaker #6 to #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match
score, s1, s2 = align(session, rseq, mseq,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align
score, seqs = NeedlemanWunsch.nw(ref, match,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in nw
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in
<listcomp>
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type
r = self.residue_at(loc)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
IndexError: vector
IndexError: vector
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
See log for complete Python traceback.
> select clear
> select add #6/A:3@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 14 residues, 1 model selected
> select up
183 atoms, 183 bonds, 25 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> show #3 models
> hide #3 models
> hide #!1 models
> select add #6/A:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
94 atoms, 93 bonds, 14 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #6 to #4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match
score, s1, s2 = align(session, rseq, mseq,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align
score, seqs = NeedlemanWunsch.nw(ref, match,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in nw
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in
<listcomp>
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type
r = self.residue_at(loc)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
IndexError: vector
IndexError: vector
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
See log for complete Python traceback.
> undo
[Repeated 9 time(s)]
> delete sel
> show #!1 models
> build start peptide "custom built" KAQAKAQAKAR -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack
Chain information for custom built #5
---
Chain | Description
A | No description available
> show #3 models
> show #4 models
> hide #4 models
> hide #3 models
> ui tool show Matchmaker
> matchmaker #5 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 polyA_full, chain A (#1) with custom built, chain A (#5), sequence
alignment score = 50.6
RMSD between 11 pruned atom pairs is 0.000 angstroms; (across all 11 pairs:
0.000)
> select add #5
82 atoms, 81 bonds, 11 residues, 1 model selected
> delete sel
> build start peptide "custom built" YAKAQAKAAKAQAKA -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 rotLib Dunbrack
Chain information for custom built #5
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #5 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 polyA_full, chain A (#1) with custom built, chain A (#5), sequence
alignment score = 71.1
RMSD between 15 pruned atom pairs is 0.000 angstroms; (across all 15 pairs:
0.000)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #5
107 atoms, 107 bonds, 15 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> open /Users/fidel.lozano@fhnw.ch/Desktop/supercoil_peptide.pdb
Chain information for supercoil_peptide.pdb #6
---
Chain | Description
A | No description available
> select #5/A:15@C
1 atom, 1 residue, 1 model selected
> select #6/A:1@N
1 atom, 1 residue, 1 model selected
> select add #5/A:15@C
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move C
> show #!1 models
> hide #!1 models
> undo
[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.
> select add #6
183 atoms, 183 bonds, 25 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #6 to #4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 288, in run_matchmaker
run(self.session, cmd)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match
score, s1, s2 = align(session, rseq, mseq,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align
score, seqs = NeedlemanWunsch.nw(ref, match,
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in nw
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 51, in
<listcomp>
"".join([s2.ss_type(i) or ' 'for i in range(len(s2))]),
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type
r = self.residue_at(loc)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
IndexError: vector
IndexError: vector
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at
return convert.residue_or_none(f(self._c_pointer, index))
See log for complete Python traceback.
> show #!1 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
89 atoms, 88 bonds, 13 residues, 1 model selected
> select up
183 atoms, 183 bonds, 25 residues, 1 model selected
> color sel orange
> color sel byhetero
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> hide #!1 models
> select clear
Drag select of 1 residues
> select clear
> select add #6/A:1
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/A:4
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/A:7
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #6/A:10
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #6/A:14
36 atoms, 32 bonds, 4 residues, 1 model selected
> select add #6/A:20
45 atoms, 40 bonds, 5 residues, 1 model selected
> select add #6/A:16
54 atoms, 48 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> select #6/A:3@CE
1 atom, 1 residue, 1 model selected
> select add #6/A:3@NZ
2 atoms, 1 residue, 1 model selected
> select clear
> save /Users/fidel.lozano@fhnw.ch/Desktop/image1.png supersample 3
> save /Users/fidel.lozano@fhnw.ch/Desktop/image2.png supersample 3
> select add #6
183 atoms, 183 bonds, 25 residues, 1 model selected
> color #6 #aa7942ff
> color #6 #ffdd00ff
> color #6 #d4b48aff
> color sel byhetero
> select clear
> select #6/A:1
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel ball
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> hide sel cartoons
> show sel cartoons
> select clear
> select #6/A:1
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:1
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #6/A:1
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #6/A:25
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select clear
> save /Users/fidel.lozano@fhnw.ch/Desktop/image3.png supersample 3
> save /Users/fidel.lozano@fhnw.ch/Desktop/image4.png supersample 3
> select add #6
183 atoms, 183 bonds, 25 residues, 1 model selected
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
82 atoms, 81 bonds, 11 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/A:25
12 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> save /Users/fidel.lozano@fhnw.ch/Desktop/image5.png supersample 3
> save /Users/fidel.lozano@fhnw.ch/Desktop/image6.png supersample 3
> save "/Users/fidel.lozano@fhnw.ch/OneDrive - FHNW/Peptides-
> NanoParticles/peptide_design/polyA_modeling.cxs"
> build start peptide mostly_supercoil_polyA2 YAKAQAK -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack
Chain information for mostly_supercoil_polyA2 #5
---
Chain | Description
A | No description available
> hide #6 models
> select add #6
183 atoms, 183 bonds, 25 residues, 1 model selected
> show #5 cartoons
> select add #5
238 atoms, 238 bonds, 32 residues, 2 models selected
> hide sel & #5 cartoons
> select clear
> open /Users/fidel.lozano@fhnw.ch/Desktop/supercoil_2.pdb
Chain information for supercoil_2.pdb #7
---
Chain | Description
A | No description available
> select add #7
64 atoms, 63 bonds, 9 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select clear
> select #7/A:1@N
1 atom, 1 residue, 1 model selected
> select #5/A:7@C
1 atom, 1 residue, 1 model selected
> select add #7/A:1@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> show #3 models
> show #6 models
> hide #6 models
> show #4 models
> select add #6
184 atoms, 183 bonds, 26 residues, 2 models selected
> select add #5
301 atoms, 301 bonds, 41 residues, 2 models selected
> select subtract #5
183 atoms, 183 bonds, 25 residues, 1 model selected
> select add #5
301 atoms, 301 bonds, 41 residues, 2 models selected
> select subtract #6
118 atoms, 118 bonds, 16 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> show sel cartoons
> select clear
> show #6 models
> hide #6 models
> save "/Users/fidel.lozano@fhnw.ch/OneDrive - FHNW/Peptides-
> NanoParticles/peptide_design/polyA_modeling.cxs"
\u2014\u2014\u2014 End of log from Thu Apr 27 15:03:48 2023 \u2014\u2014\u2014
opened ChimeraX session
> show #1.1 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #!2 models
> show #1.1 models
> hide #1.1 models
> select #1/A:12@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> ui tool show "Build Structure"
> open /Users/fidel.lozano@fhnw.ch/Desktop/polyA_long_FRET.pdb
Chain information for polyA_long_FRET.pdb #7
---
Chain | Description
A | No description available
> select add #7/A:12
43 atoms, 42 bonds, 3 residues, 3 models selected
> select up
552 atoms, 552 bonds, 51 residues, 3 models selected
> select up
624 atoms, 626 bonds, 55 residues, 3 models selected
> select down
552 atoms, 552 bonds, 51 residues, 3 models selected
> select subtract #1.1
383 atoms, 384 bonds, 26 residues, 2 models selected
> hide #7 models
> show #7 models
> ui tool show "Add Hydrogens"
> select H
219 atoms, 28 residues, 1 model selected
> hide sel atoms
> color #7 #996666ff
> color #7 #0099ccff
> color sel byhetero
[Repeated 1 time(s)]
> hide #7 models
> show #7 models
> color sel cornflower blue
> undo
> select up
431 atoms, 433 bonds, 28 residues, 1 model selected
> color sel byhetero
> color #7 #66ffffff
> color sel byhetero
> select clear
> ui tool show Matchmaker
> matchmaker #7 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 polyA_full, chain A (#1) with polyA_long_FRET.pdb, chain A (#7),
sequence alignment score = 126.5
RMSD between 25 pruned atom pairs is 1.184 angstroms; (across all 27 pairs:
1.319)
> hide #!1 models
> show #7 atoms
> select add #7
431 atoms, 433 bonds, 28 residues, 1 model selected
> select H
219 atoms, 28 residues, 1 model selected
> delete sel
> select clear
> select #7/A:16@CB
1 atom, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> toolshed show
> ui mousemode right distance
> distance #7/A:12@@serial_number=420 #7/A:15@CZ
Distance between polyA_long_FRET.pdb #7/A UNK 12 C and TYR 15 CZ: 9.700Å
> select add #7
212 atoms, 214 bonds, 1 pseudobond, 28 residues, 2 models selected
> select subtract #7
Nothing selected
> select add #7
212 atoms, 214 bonds, 1 pseudobond, 28 residues, 2 models selected
> show #2.1 models
> select clear
> color #2.1 #996600ff models
> show #!1 models
> hide #!1 models
> save "/Users/fidel.lozano@fhnw.ch/OneDrive -
> FHNW/PROJECTS/02_NanoParticles/Peptide_design/polyA_modeling.cxs"
\u2014\u2014\u2014 End of log from Fri Jan 26 10:24:23 2024 \u2014\u2014\u2014
opened ChimeraX session
> select clear
> select #7/A:15
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> ui mousemode right swapaa
> swapaa mousemode #7/A:15 TYR
[Repeated 13 time(s)]
> swapaa mousemode #7/A:13 ALA
[Repeated 2 time(s)]
> select clear
> swapaa mousemode #7/A:15 TYR
[Repeated 1 time(s)]
> select #7/A:15
12 atoms, 12 bonds, 1 residue, 1 model selected
> swapaa mousemode #7/A:15 TYR
[Repeated 2 time(s)]
> ui mousemode right swapaa
> ui mousemode right "bond rotation"
> ui mousemode right swapaa
> swapaa mousemode #7/A:15 TYR
[Repeated 6 time(s)]
> select clear
> swapaa mousemode #7/A:15 TYR
[Repeated 3 time(s)]
> swapaa mousemode #7/A:15 TRP
[Repeated 1 time(s)]
> swapaa mousemode #7/A:12 LYS
swapaa: Cannot swap non-protein residues "polyA_long_FRET.pdb #7/A UNK 12"
> swapaa mousemode #7/A:15 TRP
[Repeated 20 time(s)]
> ui mousemode right swapaa
> ui mousemode right "bond rotation"
> torsion #7/A:15@CD1,CG,CB,CA 62.12
> ui mousemode right swapaa
> swapaa mousemode #7/A:15 TRP
[Repeated 7 time(s)]
> select clear
> select #7/A:15
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> ui tool show Rotamers
> swapaa interactive sel TRP rotLib Dunbrack
polyA_long_FRET.pdb #7/A TRP 15: phi -68.9, psi -55.4 trans
Changed 468 bond radii
> hbonds #!7 & ~#!7/A:15 & ~solvent reveal true restrict #7.1 & ~@c,ca,n
0 hydrogen bonds found
> clashes #!7 & ~#!7/A:15 & ~solvent radius 0.075 reveal true restrict #7.1 &
> ~@c,ca,n
324 clashes
Must open a volume/map file first!
> swapaa #!7/A:15 TRP criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
polyA_long_FRET.pdb #!7/A TRP 15: phi -68.9, psi -55.4 trans
Applying TRP rotamer (chi angles: 179.4 84.5) to polyA_long_FRET.pdb #!7/A TRP
15
> select clear
> select #7/A:16
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:15
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show Angles/Torsions
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> ui tool show "Altloc Explorer"
> ui tool show Rotamers
> swapaa interactive sel TRP rotLib Dynameomics
polyA_long_FRET.pdb #7/A TRP 15: phi -68.9, psi -55.4 trans
Changed 117 bond radii
> clashes #!7 & ~#!7/A:15 & ~solvent radius 0.075 reveal true restrict #7.1 &
> ~@c,ca,n
107 clashes
> ui tool show Rotamers
> swapaa interactive sel TRP rotLib Dunbrack
polyA_long_FRET.pdb #7/A TRP 15: phi -68.9, psi -55.4 trans
Changed 468 bond radii
> swapaa #!7/A:15 TRP criteria 2 rotLib Dunbrack retain true
Using Dunbrack library
polyA_long_FRET.pdb #!7/A TRP 15: phi -68.9, psi -55.4 trans
Applying TRP rotamer (chi angles: 179.4 -97.7) to polyA_long_FRET.pdb #!7/A
TRP 15 using alt loc A
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #9 models
> hide #!1 models
> hide #!2 models
> hide #7 models
> show #7 models
> select add #7
214 atoms, 217 bonds, 28 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #8 models
> show #8 models
> select subtract #9
Nothing selected
> select subtract #8
Nothing selected
> select add #8
Nothing selected
> select add #9
Nothing selected
> select #7/A:15
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel TRP rotLib Dunbrack
polyA_long_FRET.pdb #7/A TRP 15: phi -68.9, psi -55.4 trans
Changed 468 bond radii
> swapaa #!7/A:15 TRP criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
polyA_long_FRET.pdb #!7/A TRP 15: phi -68.9, psi -55.4 trans
Applying TRP rotamer (chi angles: 179.4 84.5) to polyA_long_FRET.pdb #!7/A TRP
15
> select clear
[Repeated 1 time(s)]
> ui mousemode right swapaa
> ui mousemode right distance
> ui mousemode right select
> select #7@@serial_number=417
1 atom, 1 residue, 1 model selected
> ui tool show Axes/Planes/Centroids
> select add #7@@serial_number=422
2 atoms, 1 bond, 1 residue, 1 model selected
> select clear
> select #7@@serial_number=422
1 atom, 1 residue, 1 model selected
> select #7@@serial_number=417
1 atom, 1 residue, 1 model selected
> select add #7@@serial_number=422
2 atoms, 1 residue, 1 model selected
> select add #7@@serial_number=421
3 atoms, 1 residue, 1 model selected
> select add #7@@serial_number=420
4 atoms, 1 residue, 1 model selected
> select add #7@@serial_number=419
5 atoms, 1 residue, 1 model selected
> select add #7@@serial_number=418
6 atoms, 1 residue, 1 model selected
> define centroid sel radius 0.1
Centroid 'centroid' placed at [-14.8386666 13.18566688 12.25400003]
> select #!7/A:15@CE2
1 atom, 1 residue, 1 model selected
> select add #!7/A:15@CD2
2 atoms, 1 residue, 1 model selected
> select add #!7/A:15@CE3
3 atoms, 1 residue, 1 model selected
> select add #!7/A:15@CZ3
4 atoms, 1 residue, 1 model selected
> select add #!7/A:15@CH2
5 atoms, 1 residue, 1 model selected
> select add #!7/A:15@CZ2
6 atoms, 1 residue, 1 model selected
> define centroid sel radius 0.1
Centroid 'centroid' placed at [-15.78439663 5.58426493 12.45762524]
> select clear
> select #7.1
1 atom, 1 residue, 1 model selected
> ~select #7.1
Nothing selected
> select #7.1
1 atom, 1 residue, 1 model selected
> select #7.2
1 atom, 1 residue, 1 model selected
> select #7.1
1 atom, 1 residue, 1 model selected
> select add #7.2/centroid:1@centroid
2 atoms, 2 residues, 2 models selected
> distance #7.1/centroid:1#7.2/centroid:1 #7.1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 145, in _apc_report_distance
info = run(self.session, "distance %s %s" % (target_spec, item_spec))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
> select clear
No atoms selected
> select #7.1/centroid:1@centroid
1 atom, 1 residue, 1 model selected
> select add #7.2/centroid:1@centroid
2 atoms, 2 residues, 2 models selected
> distance #7.1/centroid:1#7.2/centroid:1 #7.1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 145, in _apc_report_distance
info = run(self.session, "distance %s %s" % (target_spec, item_spec))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
> ui mousemode right distance
> distance #7.1/centroid:1@centroid #7.2/centroid:1@centroid
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/mouse_dist.py", line 34, in mouse_up
self._picked_object(pick)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/mouse_dist.py", line 56, in _picked_object
run(self.session, command)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
> distance #7.1/centroid:1@centroid #7.2/centroid:1@centroid
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/mouse_dist.py", line 34, in mouse_up
self._picked_object(pick)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/mouse_dist.py", line 56, in _picked_object
run(self.session, command)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
AttributeError: 'CentroidModel' object has no attribute 'distance'
AttributeError: 'CentroidModel' object has no attribute 'distance'
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/cmd.py", line 134, in distance
dist = object.distance(a, signed=signed)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.9.11
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 Pro
Model Identifier: Mac14,9
Model Number: MPHE3SM/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 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: 25 days, 6 hours, 53 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
HP Z24n G2:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 75.00Hz
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: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 22 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker: IndexError: vector |
comment:2 by , 22 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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