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Opened 14 months ago
Closed 14 months ago
#15758 closed defect (fixed)
IndexError showing MatchMaker alignment
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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: Windows-10-10.0.19044
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/2PF_TSA_GDP-
> alignTX-ChainA.pdb
> F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/a1A_bIII_GDP-
> aligned_tsa_taxol-chainA.pdb
> F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/tsa_taxol-good-
> chainA.pdb
Summary of feedback from opening
F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/2PF_TSA_GDP-alignTX-
ChainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 10 GLY B 29 1 20
Start residue of secondary structure not found: HELIX 2 2 SER B 40 VAL B 49 1
10
Start residue of secondary structure not found: HELIX 4 4 PRO B 70 GLY B 79 1
10
Start residue of secondary structure not found: HELIX 5 5 ARG B 86 ASP B 88 1
3
Start residue of secondary structure not found: HELIX 6 6 ASN B 100 CYS B 127
1 28
180 messages similar to the above omitted
Summary of feedback from opening
F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY C 10 GLU C 27 1 18
Start residue of secondary structure not found: HELIX 2 2 ASP C 41 GLU C 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE C 47 VAL C 49 1
3
Start residue of secondary structure not found: HELIX 5 5 PRO C 70 SER C 78 1
9
Start residue of secondary structure not found: HELIX 6 6 GLY C 82 LEU C 84 1
3
197 messages similar to the above omitted
Summary of feedback from opening
F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/tsa_taxol-good-
chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 GLY A 44 THR A 51 1 8
Start residue of secondary structure not found: HELIX 16 16 GLY B 10 HIS B 28
1 19
Start residue of secondary structure not found: HELIX 17 17 ASP B 41 ASP B 45
1 5
Start residue of secondary structure not found: HELIX 18 18 ILE B 47 VAL B 49
1 3
Start residue of secondary structure not found: HELIX 19 19 THR B 55 GLY B 57
1 3
201 messages similar to the above omitted
Chain information for 2PF_TSA_GDP-alignTX-ChainA.pdb #1
---
Chain | Description
A | No description available
Chain information for a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #2
---
Chain | Description
A | No description available
Chain information for tsa_taxol-good-chainA.pdb #3
---
Chain | Description
A | No description available
> hide #3.2 models
> close #3.2
> close #2.2
> close #1.2
> hide #1.1 models
> hide #2.1 models
> hide #3.1 models
> ui tool show "Color Actions"
> set bgColor white
> show atoms
> hide cartoons
> hide (#!1-3 & (protein|nucleic)) target a
> cartoon hide #!1-3
> show (#!1-3 & ((protein&@ca)|(nucleic&@p))) target ab
> close #1.1
> close #2.1
> close #3.1
> select #2/A: 3-10,64-70,91-95,131-140,164-171,200-204
> #3/A:3-10,64-70,91-95,131-140,164-171,200-204
> #4/A:3-10,64-70,91-95,131-140,164-171,200-204
664 atoms, 666 bonds, 74 pseudobonds, 86 residues, 4 models selected
> size pseudobondRadius 0.25
Changed 5151 pseudobond radii
> select #2/A: 3003-3010,3064-3070,3091-3095,3131-3140,3164-3171,3200-3204
> #3/A:3003-3010,3064-3070,3091-3095,3131-3140,3164-3171,3200-3204
> #1/A:3003-3010,3064-3070,3091-3095,3131-3140,3164-3171,3200-3204
994 atoms, 1000 bonds, 111 pseudobonds, 129 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #1 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#1) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb, chain A (#2), sequence alignment score = 213.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 2PF_TSA_GDP-alignTX-ChainA.pdb
#1/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 43 pruned atom pairs is 0.340 angstroms; (across all 43 pairs:
0.340)
> hide #!3 models
> hide #3.2 models
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!2 target scab palette
> 0,blue:0,white:26.5469,red
13515 atoms, 1722 residues, atom seq_rmsd range 0.0173 to 88.9
> show #3.2 models
> hide #!3 models
> hide #3.2 models
> show #!3 models
> hide #!3 models
> ui tool show Matchmaker
> show #!3 models
> matchmaker #!3 & sel to #1 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#1) with tsa_taxol-good-
chainA.pdb, chain A (#3), sequence alignment score = 213.9
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: 2PF_TSA_GDP-alignTX-ChainA.pdb
#1/A, tsa_taxol-good-chainA.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 43 pruned atom pairs is 0.400 angstroms; (across all 43 pairs:
0.400)
> show #3.2 models
> hide #!3 models
> select clear
> hide #2.2 models
> hide #!2 models
> show #!3 models
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!3 target scab palette
> 0,blue:0,white:28.828,#5500ff
13669 atoms, 1731 residues, atom seq_rmsd range 0.0631 to 90.8
> color byattribute r:seq_rmsd #!3 target scab palette
> 0.285426,white:10.2753,blue:28.828,red
13669 atoms, 1731 residues, atom seq_rmsd range 0.0631 to 90.8
> color byattribute r:seq_rmsd #!3 target scab palette
> 0.285426,white:10.2753,blue:19.9798,red
13669 atoms, 1731 residues, atom seq_rmsd range 0.0631 to 90.8
> color byattribute r:seq_rmsd #!3 target scab palette
> 0.285426,white:3.42511,blue:19.9798,red
13669 atoms, 1731 residues, atom seq_rmsd range 0.0631 to 90.8
> color byattribute r:seq_rmsd #!3 target scab palette
> 0.285426,white:3.5,blue:19.9798,red
13669 atoms, 1731 residues, atom seq_rmsd range 0.0631 to 90.8
> color byattribute r:seq_rmsd #!3 target scab palette
> 0.285426,white:3.5,blue:20,red
13669 atoms, 1731 residues, atom seq_rmsd range 0.0631 to 90.8
> show #!2 models
> hide #1.2 models
> show #1.2 models
> show #2.2 models
> hide #1.2 models
> show #1.2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save
> F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/Session1betaNSheets.cxs
> hide #!1 models
> hide #!2 models
> hide #2.2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #2.2 models
> select /A: 1-2000
20423 atoms, 20891 bonds, 2584 pseudobonds, 2608 residues, 6 models selected
> hide sel & #!2 cartoons
> hide sel & #!2 atoms
> show #!3 models
> show #!1 models
> delete atoms (#!1-3 & sel)
> delete bonds (#!1-3 & sel)
> size pseudobondRadius 0.25
Changed 2567 pseudobond radii
> select #2/A: 3003-3010,3064-3070,3091-3095,3131-3140,3164-3171,3200-3204
> #3/A:3003-3010,3064-3070,3091-3095,3131-3140,3164-3171,3200-3204
> #1/A:3003-3010,3064-3070,3091-3095,3131-3140,3164-3171,3200-3204
994 atoms, 1000 bonds, 111 pseudobonds, 129 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #1 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#1) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb, chain A (#2), sequence alignment score = 213.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 2PF_TSA_GDP-alignTX-ChainA.pdb
#1/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 43 pruned atom pairs is 0.340 angstroms; (across all 43 pairs:
0.340)
> matchmaker #!3 & sel to #1 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#1) with tsa_taxol-good-
chainA.pdb, chain A (#3), sequence alignment score = 213.9
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: 2PF_TSA_GDP-alignTX-ChainA.pdb
#1/A, tsa_taxol-good-chainA.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 43 pruned atom pairs is 0.400 angstroms; (across all 43 pairs:
0.400)
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!2 target scab palette
> 0,white:6.5,red:6.5,white
6750 atoms, 860 residues, atom seq_rmsd range 0.0173 to 6.31
> color byattribute r:seq_rmsd #!3 target scab palette
> 0,white:6.5,red:6.5,white
6855 atoms, 861 residues, atom seq_rmsd range 0.0631 to 5.4
> color #1 #c7d2d0ff
> select clear
> save
> F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/Session1betaNSheets.cxs
> ui tool show "Render/Select by Attribute"
> key blue-white-red :0.02 :3.16 :6.31 showTool true
> ui mousemode right "color key"
> key blue-white-red :0 :3.16 :6.31
> key blue-white-red :0 :0 :6.31
> key blue-white-red :0 :0 :6
> key blue-white-red :0 :0 :6.
> key blue-white-red :0 :0 :6.5
> ui mousemode right translate
> save
> F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/Session1betaNSheets.cxs
> open F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/2PF_TSA_GDP-
> alignTX-ChainA.pdb
> F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/a1A_bIII_GDP-
> aligned_tsa_taxol-chainA.pdb
> F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/tsa_taxol-good-
> chainA.pdb
Summary of feedback from opening
F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/2PF_TSA_GDP-alignTX-
ChainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 10 GLY B 29 1 20
Start residue of secondary structure not found: HELIX 2 2 SER B 40 VAL B 49 1
10
Start residue of secondary structure not found: HELIX 4 4 PRO B 70 GLY B 79 1
10
Start residue of secondary structure not found: HELIX 5 5 ARG B 86 ASP B 88 1
3
Start residue of secondary structure not found: HELIX 6 6 ASN B 100 CYS B 127
1 28
180 messages similar to the above omitted
Summary of feedback from opening
F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY C 10 GLU C 27 1 18
Start residue of secondary structure not found: HELIX 2 2 ASP C 41 GLU C 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE C 47 VAL C 49 1
3
Start residue of secondary structure not found: HELIX 5 5 PRO C 70 SER C 78 1
9
Start residue of secondary structure not found: HELIX 6 6 GLY C 82 LEU C 84 1
3
197 messages similar to the above omitted
Summary of feedback from opening
F:/tsATaxol/ChimeraX/FigureSessionsNew/LateralAnalysis/tsa_taxol-good-
chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 GLY A 44 THR A 51 1 8
Start residue of secondary structure not found: HELIX 16 16 GLY B 10 HIS B 28
1 19
Start residue of secondary structure not found: HELIX 17 17 ASP B 41 ASP B 45
1 5
Start residue of secondary structure not found: HELIX 18 18 ILE B 47 VAL B 49
1 3
Start residue of secondary structure not found: HELIX 19 19 THR B 55 GLY B 57
1 3
201 messages similar to the above omitted
Chain information for 2PF_TSA_GDP-alignTX-ChainA.pdb #5
---
Chain | Description
A | No description available
Chain information for a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #6
---
Chain | Description
A | No description available
Chain information for tsa_taxol-good-chainA.pdb #7
---
Chain | Description
A | No description available
Associated 2PF_TSA_GDP-alignTX-ChainA.pdb chain A to 2PF_TSA_GDP-alignTX-
ChainA.pdb, chain A with 0 mismatches
Associated a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb chain A to a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 2PF_TSA_GDP-alignTX-ChainA.pdb
#1/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #2/A, 2PF_TSA_GDP-alignTX-
ChainA.pdb #5/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #6/A
Associated 2PF_TSA_GDP-alignTX-ChainA.pdb chain A to 2PF_TSA_GDP-alignTX-
ChainA.pdb, chain A with 0 mismatches
Associated tsa_taxol-good-chainA.pdb chain A to tsa_taxol-good-chainA.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 2: 2PF_TSA_GDP-alignTX-ChainA.pdb
#1/A, tsa_taxol-good-chainA.pdb #3/A, 2PF_TSA_GDP-alignTX-ChainA.pdb #5/A,
tsa_taxol-good-chainA.pdb #7/A
> close #1-3
Chains used in RMSD evaluation for alignment 1: 2PF_TSA_GDP-alignTX-ChainA.pdb
#5/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #6/A
Chains used in RMSD evaluation for alignment 2: 2PF_TSA_GDP-alignTX-ChainA.pdb
#5/A, tsa_taxol-good-chainA.pdb #7/A
> close #4
> show atoms
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> hide #!6 models
> hide #!7 models
> select /A: 2001-4000
20093 atoms, 20547 bonds, 2571 pseudobonds, 2575 residues, 9 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select clear
Drag select of 56 atoms, 60 bonds
> delete atoms sel
> delete bonds sel
> show #!6 models
> show #!7 models
> select /A: 2001-4000
13425 atoms, 13729 bonds, 1714 pseudobonds, 1717 residues, 6 models selected
> delete atoms (#!6-7 & sel)
> delete bonds (#!6-7 & sel)
Drag select of 61 atoms, 68 bonds
Drag select of 28 atoms, 30 bonds
Drag select of 62 atoms, 68 bonds
Drag select of 28 atoms, 30 bonds
> delete atoms sel
> delete bonds sel
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> hide sel atoms
> select #2/A: 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
> #1/A: 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204 #3/A:
> 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
Nothing selected
> select #2/A: 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
> #1/A: 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204 #3/A:
> 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
Nothing selected
> select #2/A:1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
> #1/A: 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204 #3/A:
> 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
Nothing selected
> select #5/A:1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
> #6/A: 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204 #7/A:
> 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
996 atoms, 999 bonds, 111 pseudobonds, 129 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#5) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb, chain A (#6), sequence alignment score = 179.7
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: 2PF_TSA_GDP-alignTX-ChainA.pdb
#5/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 43 pruned atom pairs is 0.358 angstroms; (across all 43 pairs:
0.358)
> ui tool show Matchmaker
> matchmaker #!7 & sel to #5 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#5) with tsa_taxol-good-
chainA.pdb, chain A (#7), sequence alignment score = 197.1
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: 2PF_TSA_GDP-alignTX-ChainA.pdb
#5/A, tsa_taxol-good-chainA.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 43 pruned atom pairs is 0.493 angstroms; (across all 43 pairs:
0.493)
> select clear
> size pseudobondRadius 0.25
Changed 2602 pseudobond radii
> color #5 #f7fafaff
> ui tool show "Render/Select by Attribute"
> key white:0.00 white:0.00 blue:1.92 showTool true
> ui mousemode right "color key"
> key white:0.00 white:0.00 blue:1.9
> key white:0.00 white:0.00 blue:1.
> key white:0.00 white:0.00 blue:1
> key white:0.00 white:0.00 blue:
> key white:0.00 white:0.00 blue:2
> ui mousemode right translate
> color byattribute r:seq_rmsd #!6 target scab palette
> 0,white:0,white:1.91704,blue
6765 atoms, 862 residues, atom seq_rmsd range 0.0375 to 22.6
> key white:0.00 white:0.00 blue:2.75 showTool true
> ui mousemode right "color key"
> key white:0.00 white:0.00 blue:3
> ui mousemode right translate
> color byattribute r:seq_rmsd #!7 target scab palette
> 0,white:0,white:2.75255,blue
6815 atoms, 871 residues, atom seq_rmsd range 0.0845 to 16.8
> color byattribute r:seq_rmsd #!7 target scab palette 0,white:0,white:3,blue
6815 atoms, 871 residues, atom seq_rmsd range 0.0845 to 16.8
> color byattribute r:seq_rmsd #!6 target scab palette
> 0.0375209,white:0.0375209,white:3,blue
6765 atoms, 862 residues, atom seq_rmsd range 0.0375 to 22.6
> color byattribute r:seq_rmsd #!6 target scab palette 0,white:0,white:3,blue
6765 atoms, 862 residues, atom seq_rmsd range 0.0375 to 22.6
> color byattribute r:seq_rmsd #!7 target scab palette
> 0.0845228,white:0.0845228,white:3,blue
6815 atoms, 871 residues, atom seq_rmsd range 0.0845 to 16.8
> select clear
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!6 target scab palette 0,blue:0,white:3,red
> noValueColor grey
6765 atoms, 862 residues, atom seq_rmsd range 0.0375 to 22.6
> ui tool show "Render/Select by Attribute"
> select add #1
1 model selected
> hide #1 models
> select subtract #1
Nothing selected
> select #5/A:1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
> #6/A: 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204 #7/A:
> 1003-1010,1064-1070,1091-1095,1131-1140,1164-1171,1200-1204
996 atoms, 999 bonds, 111 pseudobonds, 129 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#5) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb, chain A (#6), sequence alignment score = 179.7
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: 2PF_TSA_GDP-alignTX-ChainA.pdb
#5/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 43 pruned atom pairs is 0.358 angstroms; (across all 43 pairs:
0.358)
> ui tool show Matchmaker
> matchmaker #!6 to #5 alg Smith-Waterman showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
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 2PF_TSA_GDP-alignTX-ChainA.pdb (#5) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb (#6), sequence alignment score = 7307.7
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: 2PF_TSA_GDP-alignTX-ChainA.pdb
#5/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 857 pruned atom pairs is 0.463 angstroms; (across all 860 pairs:
0.823)
> matchmaker #!6 & sel to #5 & sel alg Smith-Waterman showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
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 2PF_TSA_GDP-alignTX-ChainA.pdb (#5) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb (#6), sequence alignment score = 179.7
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 171, in <lambda>
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 303, in run_matchmaker
run(self.session, cmd)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 742, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 547, in match
residues[i] = r
~~~~~~~~^^^
IndexError: list assignment index out of range
IndexError: list assignment index out of range
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 547, in match
residues[i] = r
~~~~~~~~^^^
See log for complete Python traceback.
> matchmaker #!6 & sel to #5 & sel 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 2PF_TSA_GDP-alignTX-ChainA.pdb, chain A (#5) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb, chain A (#6), sequence alignment score = 179.7
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: 2PF_TSA_GDP-alignTX-ChainA.pdb
#5/A, a1A_bIII_GDP-aligned_tsa_taxol-chainA.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 43 pruned atom pairs is 0.358 angstroms; (across all 43 pairs:
0.358)
> matchmaker #!6 & sel to #5 & sel alg Smith-Waterman showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
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 2PF_TSA_GDP-alignTX-ChainA.pdb (#5) with a1A_bIII_GDP-
aligned_tsa_taxol-chainA.pdb (#6), sequence alignment score = 179.7
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 171, in <lambda>
bbox.button(qbbox.Apply).clicked.connect(lambda *args:
self.run_matchmaker(apply=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\tool.py", line 303, in run_matchmaker
run(self.session, cmd)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 742, in cmd_match
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 547, in match
residues[i] = r
~~~~~~~~^^^
IndexError: list assignment index out of range
IndexError: list assignment index out of range
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\match_maker\match.py", line 547, in match
residues[i] = r
~~~~~~~~^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.9126
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 3540
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,985,317,376
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 14 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → IndexError showing MatchMaker alignment |
comment:2 by , 14 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Fix: https://github.com/RBVI/ChimeraX/commit/9fd63ea4567eeaa435352961091c1e76f5aa7238