The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3rc202110261847 (2021-10-26 18:47:13 UTC)
Description
fetched another alphafold model, starting from a session that had an alphafold model in it (although it was closed in between, if that matters)
Log:
UCSF ChimeraX version: 1.3rc202110261847 (2021-10-26)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/meng/Desktop/modelloops2.cxs format session
Log from Tue Oct 26 15:45:43 2021UCSF ChimeraX version: 1.3.dev202110261153
(2021-10-26)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/meng/Desktop/modelloops.cxs format session
Log from Tue Oct 26 12:29:36 2021UCSF ChimeraX version: 1.3.dev202110261153
(2021-10-26)
© 2016-2021 Regents of the University of California. All rights reserved.
> open modell*cxs
Log from Mon Oct 25 18:04:14 2021
> open /Users/meng/Desktop/startup.cxc
> alias reset view orient; view initial
> alias start tool show $1
> alias whereprefs info path user unversioned config
> alias captut open help:user/tutorials/binding-sites.html#cap-example
> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available
> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available
> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html
> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html
> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"
executed startup.cxc
UCSF ChimeraX version: 1.3.dev202110231141 (2021-10-23)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ltut
> open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html
Opened https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
modeling.html
> open 1t2p
1t2p title:
Crystal structure of Sortase A from Staphylococcus aureus [more info...]
Chain information for 1t2p #1
---
Chain | Description | UniProt
A B C | sortase | Q9S446_STAAU
1t2p mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> select /A:62-206
1155 atoms, 1177 bonds, 145 residues, 1 model selected
> select /B:61-206
1091 atoms, 1111 bonds, 1 pseudobond, 138 residues, 2 models selected
> select /C:62-206
1151 atoms, 1173 bonds, 145 residues, 1 model selected
> select clear
> select /C:62-206
1151 atoms, 1173 bonds, 145 residues, 1 model selected
> select clear
[Repeated 4 time(s)]
> select /B:206
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select /B:206
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select /B:61-206
1091 atoms, 1111 bonds, 1 pseudobond, 138 residues, 2 models selected
> select clear
> sequence chain /B
Alignment identifier is 1/B
> ui tool show "Model Loops"
[Repeated 2 time(s)]
> modeller refine 1/B:1:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16351975758331040400535
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16351975758331040400535
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service16351975758331040400535 finished
Parameters
---
Chain pairing | ss
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 1t2p, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 728.6
RMSD between 138 pruned atom pairs is 0.095 angstroms; (across all 138 pairs:
0.095)
Parameters
---
Chain pairing | ss
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 1t2p, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 734.6
RMSD between 138 pruned atom pairs is 0.087 angstroms; (across all 138 pairs:
0.087)
Parameters
---
Chain pairing | ss
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 1t2p, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 734.6
RMSD between 138 pruned atom pairs is 0.055 angstroms; (across all 138 pairs:
0.055)
Associated chain_B chain B to chain B with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_B
---
Chain | Description
2.1/B 2.2/B 2.3/B | No description available
> select clear
> windowsize
window size 425 455
> windowsize
window size 454 455
> windowsize 455 455
> split #1
Split 1t2p (#1) into 3 models
Chain information for 1t2p A #1.1
---
Chain | Description
A | No description available
Chain information for 1t2p B #1.2
---
Chain | Description
B | No description available
Chain information for 1t2p C #1.3
---
Chain | Description
C | No description available
> mmaker #1.1 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with 1t2p A, chain A (#1.1), sequence
alignment score = 669.4
RMSD between 120 pruned atom pairs is 0.699 angstroms; (across all 137 pairs:
1.217)
> mmaker #1.3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with 1t2p C, chain C (#1.3), sequence
alignment score = 663.4
RMSD between 125 pruned atom pairs is 0.786 angstroms; (across all 137 pairs:
1.139)
> view
> undo
> color bfactor #1
3759 atoms, 790 residues, atom bfactor range 4.5 to 155
> undo
> color bfactor #1
3759 atoms, 790 residues, atom bfactor range 4.5 to 155
> save bfactor.png
> undo
> save compare1.png
[Repeated 2 time(s)]
> color bfactor #1
3759 atoms, 790 residues, atom bfactor range 4.5 to 155
> save bfactor.png
> undo
> sequence dissociate ~#1.2
Disassociated chain_B (2.3) chain B from chain B
Disassociated chain_B (2.2) chain B from chain B
Disassociated chain_B (2.1) chain B from chain B
1t2p A #1.1/A not associated with any alignment
1t2p C #1.3/C not associated with any alignment
> sequence dissociate ~#1.2
chain_B #2.3/B not associated with any alignment
chain_B #2.2/B not associated with any alignment
chain_B #2.1/B not associated with any alignment
1t2p A #1.1/A not associated with any alignment
1t2p C #1.3/C not associated with any alignment
> close session
> open 1t2p format mmcif fromDatabase pdb
1t2p title:
Crystal structure of Sortase A from Staphylococcus aureus [more info...]
Chain information for 1t2p #1
---
Chain | Description | UniProt
A B C | sortase | Q9S446_STAAU
1t2p mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> sequence chain /B
Alignment identifier is 1/B
> ui tool show "Model Loops"
> modeller refine 1/B:1:internal-missing numModels 3 fast false
> adjacentFlexible 1 protocol standard
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service1635200562788-1526788427
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service1635200562788-1526788427
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service1635200562788-1526788427 finished
Parameters
---
Chain pairing | ss
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 1t2p, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 728.6
RMSD between 138 pruned atom pairs is 0.095 angstroms; (across all 138 pairs:
0.095)
Parameters
---
Chain pairing | ss
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 1t2p, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 734.6
RMSD between 138 pruned atom pairs is 0.087 angstroms; (across all 138 pairs:
0.087)
Parameters
---
Chain pairing | ss
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 1t2p, chain B (#1) with chain_B, chain B (#), sequence alignment
score = 734.6
RMSD between 138 pruned atom pairs is 0.055 angstroms; (across all 138 pairs:
0.055)
Associated chain_B chain B to chain B with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_B
---
Chain | Description
2.1/B 2.2/B 2.3/B | No description available
> split #1
Split 1t2p (#1) into 3 models
Chain information for 1t2p A #1.1
---
Chain | Description
A | No description available
Chain information for 1t2p B #1.2
---
Chain | Description
B | No description available
Chain information for 1t2p C #1.3
---
Chain | Description
C | No description available
> mmaker #1.1 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with 1t2p A, chain A (#1.1), sequence
alignment score = 669.4
RMSD between 120 pruned atom pairs is 0.699 angstroms; (across all 137 pairs:
1.217)
> mmaker #1.3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with 1t2p C, chain C (#1.3), sequence
alignment score = 663.4
RMSD between 125 pruned atom pairs is 0.786 angstroms; (across all 137 pairs:
1.139)
> color bfactor #1
3759 atoms, 790 residues, atom bfactor range 4.5 to 155
> undo
> sequence dissociate #2
Disassociated chain_B (2.1) chain B from chain B
Disassociated chain_B (2.2) chain B from chain B
Disassociated chain_B (2.3) chain B from chain B
> sequence associate #1.2
Associated 1t2p B (1.2) chain B to chain B with 0 mismatches
> hide #!2 models
> ui tool show "Model Loops"
> modeller refine 1/B:1:internal-missing numModels 3 fast false
> adjacentFlexible 2 protocol standard
Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v10.1) for
protein structure modeling
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service
Opal job id: appModeller9v8Service16352060598971357719412
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appModeller9v8Service16352060598971357719412
stdout.txt = standard output
stderr.txt = standard error
Modeller job ID appModeller9v8Service16352060598971357719412 finished
Parameters
---
Chain pairing | ss
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 1t2p B, chain B (#1.2) with chain_B, chain B (#), sequence
alignment score = 692.6
RMSD between 136 pruned atom pairs is 0.063 angstroms; (across all 138 pairs:
0.517)
Parameters
---
Chain pairing | ss
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 1t2p B, chain B (#1.2) with chain_B, chain B (#), sequence
alignment score = 692.6
RMSD between 137 pruned atom pairs is 0.055 angstroms; (across all 138 pairs:
0.312)
Parameters
---
Chain pairing | ss
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 1t2p B, chain B (#1.2) with chain_B, chain B (#), sequence
alignment score = 692.6
RMSD between 136 pruned atom pairs is 0.091 angstroms; (across all 138 pairs:
0.567)
Associated chain_B chain B to chain B with 0 mismatches
[Repeated 2 time(s)] Chain information for chain_B
---
Chain | Description
3.1/B 3.2/B 3.3/B | No description available
> show #!2 models
> hide #!2 models
> transparency 60 #1 targ r
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #1 60 target r
> transparency #1 75 target r
> transparency #1 65 target r
> transparency #1 0 target r
> select #3.3
1306 atoms, 1182 bonds, 292 residues, 1 model selected
> select clear
> lighting full
> lighting soft
[Repeated 1 time(s)]
> lighting gentle
> clashes #3.3 restrict #3.3
47 clashes
> clashes #3.2 restrict #3.2
3 clashes
> clashes #3.1 restrict #3.1
3 clashes
> lighting simple
> help clashes
> ~clashes
> clashes #3.3 restrict #3.3 makePseudobonds false
47 clashes
> clashes #3.2 restrict #3.2 makePseudobonds false
3 clashes
> clashes #3.1 restrict #3.1 makePseudobonds false
3 clashes
> hide #!1 models
> show #!1 models
> lighting gentle
> lighting simple
> lighting gentle
> lighting simple
> save modelloops.cxs
——— End of log from Mon Oct 25 18:04:14 2021 ———
opened ChimeraX session
> windowsize 455 455
[Repeated 5 time(s)]
> color #3 hot pink
> color #3 plum
> color #3 hot pink
> undo
[Repeated 3 time(s)]No undo action is available
> color #3 hot pink
> save modelloops.cxs
——— End of log from Tue Oct 26 12:29:36 2021 ———
opened ChimeraX session
> ltut
> open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html
Opened https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
modeling.html
> blastprotein #1/A
ChimeraX REST job id: job_g66jfd60
BlastProtein finished.
Parsing BLAST results.
> open pdb:1T2W
Summary of feedback from opening 1T2W fetched from pdb
---
warnings | Unknown polymer entity '2' near line 4355
Unknown polymer entity '3' near line 4363
Unknown polymer entity '4' near line 4370
Unknown polymer entity '5' near line 4379
Unknown polymer entity '6' near line 4386
Atom OXT is not in the residue template for GLY /A:335
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
1t2w title:
Crystal Structure of Sortase A in Complex with a LPETG peptide [more info...]
Chain information for 1t2w #4
---
Chain | Description
A B C | sortase
1t2w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| software_defined_assembly
> matchmaker #4/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 1t2w, chain A (#4), sequence alignment
score = 715.3
RMSD between 134 pruned atom pairs is 0.410 angstroms; (across all 145 pairs:
1.687)
> delete #4/B,C
> hide #!1 models
> show #!2 models
> windowsize 455 455
> hide #4/A & ~ligand
> hide #!3 models
> show #!3 models
> style ligand sphere
Changed 35 atom styles
> alphafold match
Missing or invalid "sequences" argument: Sequences argument is empty.
> alphafold match #1/a
1 AlphaFold model found using sequence similarity searches: Q2FV99 (chain A)
AlphaFold chains matching 1t2p A
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | SRTA_STAA8 | Q2FV99 | 3.91 | 145 | 145 | 100
Opened 1 AlphaFold model
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> style ligand stick
Changed 35 atom styles
> ribbon ligand
> hide ligand
> color ligand red
> show ligand
> ~ribbon ligand
> close #4,5
> blastprotein #1/A
ChimeraX REST job id: job_uw5e76c0
> blastprotein #1/A
ChimeraX REST job id: job_ct81cu66
BlastProtein finished.
Parsing BLAST results.
BlastProtein finished.
Parsing BLAST results.
> windowsize 455 455
> view
> show #!1 models
> show #!2 models
> show #!3 models
> open pdb:1T2W
Summary of feedback from opening 1T2W fetched from pdb
---
warnings | Unknown polymer entity '2' near line 4355
Unknown polymer entity '3' near line 4363
Unknown polymer entity '4' near line 4370
Unknown polymer entity '5' near line 4379
Unknown polymer entity '6' near line 4386
Atom OXT is not in the residue template for GLY /A:335
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
note | Fetching compressed mmCIF 1t2w from
http://files.rcsb.org/download/1t2w.cif
1t2w title:
Crystal Structure of Sortase A in Complex with a LPETG peptide [more info...]
Chain information for 1t2w #4
---
Chain | Description
A B C | sortase
1t2w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| software_defined_assembly
> matchmaker #4/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 1t2w, chain A (#4), sequence alignment
score = 715.3
RMSD between 134 pruned atom pairs is 0.410 angstroms; (across all 145 pairs:
1.687)
> ui dockable false bp2
> color ligand red
> delete #4/B,C
> hide #4/A & ~ligand
> windwosize 455 455
Unknown command: windwosize 455 455
> windowsize 455 455
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #!1.2 models
> select ligand
35 atoms, 35 bonds, 5 residues, 1 model selected
> select clear
> windowsize 455 455
> hide #!4 models
> show #1.1 models
> show #!1.2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #1.3 models
> show #1.1 models
> show #1.3 models
> hide #1.1 models
> hide #1.3 models
> show #1.1 models
> show #1.3 models
> hide #!1.2 models
> hide #1.3 models
> hide #1.1 models
> show #!1.2 models
> sequence chain /b
Chains must have same sequence
> sequence chain #1/b
Alignment identifier is 1.2/B
> windowsize 455 455
> show #1.1 models
> hide #1.1 models
> show #1.3 models
> hide #1.3 models
> show #1.1 models
> show #1.3 models
> mmaker #1.1 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with 1t2p A, chain A (#1.1), sequence
alignment score = 669.4
RMSD between 120 pruned atom pairs is 0.699 angstroms; (across all 137 pairs:
1.217)
> mmaker #1.3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with 1t2p C, chain C (#1.3), sequence
alignment score = 663.4
RMSD between 125 pruned atom pairs is 0.786 angstroms; (across all 137 pairs:
1.139)
> hide #1.1 models
> hide #1.3 models
> lighting shadows true
> lighting shadows false
> show #1.1 models
> show #1.3 models
> undo
[Repeated 10 time(s)]No undo action is available
> undo
No undo action is available
> help undo
> dissoc #1
Unknown command: dissoc #1
> sequence dissociate #1
1t2p A #1.1/A not associated with any alignment
Disassociated 1t2p B (1.2) chain B from chain B
1t2p C #1.3/C not associated with any alignment
> sequence associate #1,2
Associated 1t2p A (1.1) chain A to chain B with 1 mismatch or gap
Associated 1t2p B (1.2) chain B to chain B with 0 mismatches
Associated 1t2p C (1.3) chain C to chain B with 1 mismatch or gap
Associated chain_B (2.1) chain B to chain B with 0 mismatches and/or gaps
Associated chain_B (2.2) chain B to chain B with 0 mismatches and/or gaps
Associated chain_B (2.3) chain B to chain B with 0 mismatches and/or gaps
> sequence dissociate #1,2
Disassociated 1t2p A (1.1) chain A from chain B
Disassociated 1t2p B (1.2) chain B from chain B
Disassociated 1t2p C (1.3) chain C from chain B
Disassociated chain_B (2.1) chain B from chain B
Disassociated chain_B (2.2) chain B from chain B
Disassociated chain_B (2.3) chain B from chain B
> aassoc #3
Unknown command: sequence aassoc #3
> sequence associate #3
Associated chain_B (3.1) chain B to chain B with 0 mismatches and/or gaps
Associated chain_B (3.2) chain B to chain B with 0 mismatches and/or gaps
Associated chain_B (3.3) chain B to chain B with 0 mismatches and/or gaps
> show #1.1 models
> show #1.3 models
> close #4
> mmaker #3.3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 136 pruned atom pairs is 0.091 angstroms; (across all 138 pairs:
0.567)
> mmaker #3.3 to #1.2 iter 1.0
> matchmaker #3.3 to #1.2 iter 1.0
Expected a keyword
> mmaker #3.3 to #1.2 cut 1.0
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 | 1
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 135 pruned atom pairs is 0.019 angstroms; (across all 138 pairs:
0.566)
> mmaker #3.3 to #1.2 cut 1.5
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 | 1.5
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 136 pruned atom pairs is 0.091 angstroms; (across all 138 pairs:
0.567)
> mmaker #3.3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 136 pruned atom pairs is 0.091 angstroms; (across all 138 pairs:
0.567)
> mmaker #3.3 to #1.2 cut 1.0
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 | 1
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 135 pruned atom pairs is 0.019 angstroms; (across all 138 pairs:
0.566)
> mmaker #3.3 to #1.2 cut .5
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 | 0.5
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 135 pruned atom pairs is 0.019 angstroms; (across all 138 pairs:
0.566)
> mmaker #3.3 to #1.2 cut 1.5
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 | 1.5
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 136 pruned atom pairs is 0.091 angstroms; (across all 138 pairs:
0.567)
> cut 1.0
Unknown command: cut 1.0
> mmaker #3.3 to #1.2 cut 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 | 1
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 135 pruned atom pairs is 0.019 angstroms; (across all 138 pairs:
0.566)
> mmaker #3.3 to #1.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p B, chain B (#1.2) with chain_B, chain B (#3.3), sequence
alignment score = 692.6
RMSD between 136 pruned atom pairs is 0.091 angstroms; (across all 138 pairs:
0.567)
> hide #1.1 models
> hide #1.3 models
> show #1.1 models
> show #1.3 models
> hide #1.1 models
> hide #1.3 models
> show #1.1 models
> show #1.3 models
> open pdb:1T2W
Summary of feedback from opening 1T2W fetched from pdb
---
warnings | Unknown polymer entity '2' near line 4355
Unknown polymer entity '3' near line 4363
Unknown polymer entity '4' near line 4370
Unknown polymer entity '5' near line 4379
Unknown polymer entity '6' near line 4386
Atom OXT is not in the residue template for GLY /A:335
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
note | Fetching compressed mmCIF 1t2w from
http://files.rcsb.org/download/1t2w.cif
1t2w title:
Crystal Structure of Sortase A in Complex with a LPETG peptide [more info...]
Chain information for 1t2w #4
---
Chain | Description
A B C | sortase
1t2w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| software_defined_assembly
> matchmaker #4/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 1t2w, chain A (#4), sequence alignment
score = 715.3
RMSD between 134 pruned atom pairs is 0.410 angstroms; (across all 145 pairs:
1.687)
> ltut
> open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html
Opened https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
modeling.html
> delete #4/B,C
> hide #4/A & ~ligand
> color ligand red
> hide #1.1 models
> show #!2 models
> clashes #1.1 restrict ligand makePseudobonds false
No clashes
> clashes #1.3 restrict ligand makePseudobonds false
15 clashes
> show #1.1 models
> select ligand
35 atoms, 35 bonds, 5 residues, 1 model selected
> clashes ligand restrict #1.1 reveal true
62 clashes
> hide ~ligand
> ~clashes
> select clear
> clashes ligand restrict #1.1 makePseudobonds false
62 clashes
> clashes ligand restrict #1.3 makePseudobonds false
15 clashes
> clashes ligand restrict #1.2 makePseudobonds false
No clashes
> clashes ligand restrict #1.3 makePseudobonds false
15 clashes
> clashes ligand restrict #1.3 reveal true
15 clashes
> clashes ligand restrict #1.3 & protein reveal true
No clashes
> clashes ligand restrict #1.1 & protein makePseudobonds false
48 clashes
> clashes ligand restrict #1.1 & protein makePseudobonds false
48 clashes
> clashes ligand restrict #1.2 & protein makePseudobonds false
No clashes
> clashes ligand restrict #1.3 & protein makePseudobonds false
No clashes
> clashes ligand restrict #2.1 makePseudobonds false
No clashes
> clashes ligand restrict #2.2 makePseudobonds false
No clashes
> clashes ligand restrict #2.3 makePseudobonds false
No clashes
> clashes ligand restrict #2.3 makePseudobonds false
No clashes
> clashes ligand restrict #2.2 makePseudobonds false
No clashes
> clashes ligand restrict #2.1 makePseudobonds false
No clashes
> clashes ligand restrict #3.1 makePseudobonds false
No clashes
> clashes ligand restrict #3.2 makePseudobonds false
No clashes
> clashes ligand restrict #3.3 makePseudobonds false
No clashes
> clashes ligand restrict #3.3 reveal true
53 clashes
> clashes ligand restrict #3.3 makePseudobonds false
53 clashes
> ~clashes
> clashes ligand restrict #3.2 makePseudobonds false
No clashes
> clashes ligand restrict #3.1 makePseudobonds false
3 clashes
> clashes ligand restrict #3.1 makePseudobonds false
No clashes
> clashes ligand restrict #3.3 makePseudobonds false
No clashes
> clashes ligand restrict #3.3 makePseudobonds false
53 clashes
> clashes ligand restrict #3.1 makePseudobonds false
3 clashes
> clashes ligand restrict #3.2make f
Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an
atoms specifier
> clashes ligand restrict #3.2 makePseudobonds false
No clashes
> clashes ligand restrict #3.3 makePseudobonds false
53 clashes
> clashes ligand restrict #2.1 makePseudobonds false
No clashes
> clashes ligand restrict #2.2 makePseudobonds false
No clashes
> clashes ligand restrict #2.3 makePseudobonds false
No clashes
> clashes ligand restrict #1.1 makePseudobonds false
62 clashes
> clashes ligand restrict #1.1 & protein makePseudobonds false
48 clashes
> clashes ligand restrict #1.2 & protein makePseudobonds false
No clashes
> clashes ligand restrict #1.3 & protein makePseudobonds false
No clashes
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #!1.2 models
> hide solvent
> windowsize 455 455
> alphafold match #1/B
1 AlphaFold model found using sequence similarity searches: Q2FV99 (chain B)
AlphaFold chains matching 1t2p B
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
B | SRTA_STAA8 | Q2FV99 | 3.36 | 146 | 138 | 100
Opened 1 AlphaFold model
> show #!1.2 models
> hide #1.3 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!1 models
> show #!1 models
> save modelloops2.cxs
——— End of log from Tue Oct 26 15:45:43 2021 ———
opened ChimeraX session
> windowsize
window size 455 455
> clashes ligand restrict #1.1 & protein makePseudobonds false ignoreHidden f
Expected a keyword
> open pdb:1IJA
1ija title:
Structure of Sortase [more info...]
Chain information for 1ija
---
Chain | Description | UniProt
6.1/A 6.2/A 6.3/A 6.4/A 6.5/A 6.6/A 6.7/A 6.8/A 6.9/A 6.10/A 6.11/A 6.12/A
6.13/A 6.14/A 6.15/A 6.16/A 6.17/A 6.18/A 6.19/A 6.20/A 6.21/A 6.22/A 6.23/A
6.24/A 6.25/A | Sortase | Q9S446_STAAU
> matchmaker #6/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.1), sequence
alignment score = 683.8
RMSD between 112 pruned atom pairs is 1.041 angstroms; (across all 145 pairs:
2.060)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.2), sequence
alignment score = 662.2
RMSD between 109 pruned atom pairs is 1.070 angstroms; (across all 145 pairs:
2.188)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.3), sequence
alignment score = 676.6
RMSD between 114 pruned atom pairs is 1.023 angstroms; (across all 145 pairs:
2.214)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.4), sequence
alignment score = 653.2
RMSD between 120 pruned atom pairs is 1.092 angstroms; (across all 145 pairs:
2.167)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.5), sequence
alignment score = 665.8
RMSD between 102 pruned atom pairs is 0.992 angstroms; (across all 145 pairs:
2.329)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.6), sequence
alignment score = 669.4
RMSD between 115 pruned atom pairs is 1.077 angstroms; (across all 145 pairs:
2.016)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.7), sequence
alignment score = 676.6
RMSD between 108 pruned atom pairs is 1.045 angstroms; (across all 145 pairs:
2.367)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.8), sequence
alignment score = 649.6
RMSD between 113 pruned atom pairs is 1.104 angstroms; (across all 145 pairs:
2.228)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.9), sequence
alignment score = 662.2
RMSD between 112 pruned atom pairs is 1.014 angstroms; (across all 145 pairs:
2.325)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.10), sequence
alignment score = 661.6
RMSD between 107 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
2.413)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.11), sequence
alignment score = 641.8
RMSD between 111 pruned atom pairs is 1.020 angstroms; (across all 145 pairs:
2.165)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.12), sequence
alignment score = 656.8
RMSD between 112 pruned atom pairs is 1.008 angstroms; (across all 145 pairs:
2.252)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.13), sequence
alignment score = 660.4
RMSD between 118 pruned atom pairs is 1.062 angstroms; (across all 145 pairs:
2.305)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.14), sequence
alignment score = 665.8
RMSD between 109 pruned atom pairs is 1.009 angstroms; (across all 145 pairs:
2.266)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.15), sequence
alignment score = 662.2
RMSD between 111 pruned atom pairs is 1.001 angstroms; (across all 145 pairs:
2.371)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.16), sequence
alignment score = 680.2
RMSD between 110 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
2.178)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.17), sequence
alignment score = 655
RMSD between 120 pruned atom pairs is 1.075 angstroms; (across all 145 pairs:
1.846)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.18), sequence
alignment score = 662.2
RMSD between 113 pruned atom pairs is 1.064 angstroms; (across all 145 pairs:
2.259)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.19), sequence
alignment score = 658.6
RMSD between 104 pruned atom pairs is 1.107 angstroms; (across all 145 pairs:
2.536)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.20), sequence
alignment score = 673
RMSD between 114 pruned atom pairs is 1.001 angstroms; (across all 145 pairs:
2.345)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.21), sequence
alignment score = 662.8
RMSD between 112 pruned atom pairs is 1.073 angstroms; (across all 145 pairs:
2.375)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.22), sequence
alignment score = 649.6
RMSD between 111 pruned atom pairs is 1.000 angstroms; (across all 145 pairs:
2.188)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.23), sequence
alignment score = 673
RMSD between 111 pruned atom pairs is 1.065 angstroms; (across all 145 pairs:
2.372)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.24), sequence
alignment score = 673
RMSD between 115 pruned atom pairs is 1.083 angstroms; (across all 145 pairs:
2.176)
Matchmaker 1t2p A, chain A (#1.1) with 1ija, chain A (#6.25), sequence
alignment score = 667
RMSD between 107 pruned atom pairs is 1.007 angstroms; (across all 145 pairs:
2.376)
> close #6
> open 2kid
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
6.1/A 6.2/A 6.3/A 6.4/A 6.5/A 6.6/A 6.7/A 6.8/A 6.9/A 6.10/A 6.11/A 6.12/A
6.13/A 6.14/A 6.15/A 6.16/A 6.17/A 6.18/A 6.19/A 6.20/A | Sortase |
Q9S446_STAAU
6.1/C | (PHQ)LPA(B27) peptide |
6.2/C 6.3/C 6.4/C 6.5/C 6.6/C 6.7/C 6.8/C 6.9/C 6.10/C 6.11/C 6.12/C 6.13/C
6.14/C 6.15/C 6.16/C 6.17/C 6.18/C 6.19/C 6.20/C | (PHQ)LPA(B27) peptide |
> close #6
> open pdb:2KID
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
6.1/A 6.2/A 6.3/A 6.4/A 6.5/A 6.6/A 6.7/A 6.8/A 6.9/A 6.10/A 6.11/A 6.12/A
6.13/A 6.14/A 6.15/A 6.16/A 6.17/A 6.18/A 6.19/A 6.20/A | Sortase |
Q9S446_STAAU
6.1/C 6.2/C 6.3/C 6.4/C 6.5/C 6.6/C 6.7/C 6.8/C 6.9/C 6.10/C 6.11/C 6.12/C
6.13/C 6.14/C 6.15/C 6.16/C 6.17/C 6.18/C 6.19/C 6.20/C | (PHQ)LPA(B27)
peptide |
> matchmaker #6/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.1), sequence
alignment score = 644.2
RMSD between 104 pruned atom pairs is 0.991 angstroms; (across all 145 pairs:
4.403)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.2), sequence
alignment score = 665.2
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.228)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.3), sequence
alignment score = 672.4
RMSD between 105 pruned atom pairs is 0.959 angstroms; (across all 145 pairs:
4.361)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.4), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.342)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.5), sequence
alignment score = 662.2
RMSD between 107 pruned atom pairs is 0.965 angstroms; (across all 145 pairs:
4.238)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.6), sequence
alignment score = 651.4
RMSD between 109 pruned atom pairs is 0.974 angstroms; (across all 145 pairs:
4.293)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.7), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.968 angstroms; (across all 145 pairs:
4.330)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.8), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
4.344)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.9), sequence
alignment score = 669.4
RMSD between 104 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.316)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.10), sequence
alignment score = 679
RMSD between 108 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.261)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.11), sequence
alignment score = 641.2
RMSD between 106 pruned atom pairs is 0.952 angstroms; (across all 145 pairs:
4.335)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.12), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.983 angstroms; (across all 145 pairs:
4.326)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.13), sequence
alignment score = 641.2
RMSD between 101 pruned atom pairs is 0.902 angstroms; (across all 145 pairs:
4.394)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.14), sequence
alignment score = 665.2
RMSD between 103 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.465)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.15), sequence
alignment score = 640.6
RMSD between 105 pruned atom pairs is 1.003 angstroms; (across all 145 pairs:
4.384)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.16), sequence
alignment score = 672.4
RMSD between 106 pruned atom pairs is 0.999 angstroms; (across all 145 pairs:
4.393)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.17), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.282)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.18), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 1.033 angstroms; (across all 145 pairs:
4.286)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.19), sequence
alignment score = 655.6
RMSD between 105 pruned atom pairs is 0.909 angstroms; (across all 145 pairs:
4.298)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#6.20), sequence
alignment score = 662.2
RMSD between 105 pruned atom pairs is 0.926 angstroms; (across all 145 pairs:
4.324)
> select /C
2780 atoms, 2713 bonds, 354 residues, 21 models selected
> label ligand
> label delete
> label ligand height 1
> label delete
> hide #5.2-end models
> hide #6.2-end models
> show #6.2-end models
> close #6.2-end
> label /C height 1
> label ligand height 1
> label delete
> label /c
> show /c
> ~ribbon /c
> hide protein target r
> label ligand height 1
> label ligand height 1 color red
Downloading file 1-s2.0-S0021925819548141-main.pdf
> show protein target r
> hide #!5 models
> hide #5.1 models
> hide #!6 models
> hide #!1.2 models
> hide #!1 models
> mlp #4
Map values for surface "1t2w_A SES surface": minimum -27.62, mean -5.662,
maximum 21.7
> surface close
> hide #!4 models
> show #!6 models
> mlp #6
Map values for surface "2kid_A SES surface": minimum -26.95, mean -3.461,
maximum 25.19
Map values for surface "2kid_C SES surface": minimum -10.42, mean 68.67,
maximum 184.8
> surface close
> mlp #6/a
Map values for surface "2kid_A SES surface": minimum -26.95, mean -3.461,
maximum 25.19
> surface close
> ~select
Nothing selected
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #!6 models
> show #!2 models
> show #!3 models
> show #!1.2 models
> hide #!2 models
> hide #!3 models
> close #5,6
> open pdb:2KID
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A
5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A | Sortase |
Q9S446_STAAU
5.1/C 5.2/C 5.3/C 5.4/C 5.5/C 5.6/C 5.7/C 5.8/C 5.9/C 5.10/C 5.11/C 5.12/C
5.13/C 5.14/C 5.15/C 5.16/C 5.17/C 5.18/C 5.19/C 5.20/C | (PHQ)LPA(B27)
peptide |
> matchmaker #5/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.1), sequence
alignment score = 644.2
RMSD between 104 pruned atom pairs is 0.991 angstroms; (across all 145 pairs:
4.403)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.2), sequence
alignment score = 665.2
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.228)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.3), sequence
alignment score = 672.4
RMSD between 105 pruned atom pairs is 0.959 angstroms; (across all 145 pairs:
4.361)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.4), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.342)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.5), sequence
alignment score = 662.2
RMSD between 107 pruned atom pairs is 0.965 angstroms; (across all 145 pairs:
4.238)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.6), sequence
alignment score = 651.4
RMSD between 109 pruned atom pairs is 0.974 angstroms; (across all 145 pairs:
4.293)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.7), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.968 angstroms; (across all 145 pairs:
4.330)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.8), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
4.344)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.9), sequence
alignment score = 669.4
RMSD between 104 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.316)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.10), sequence
alignment score = 679
RMSD between 108 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.261)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.11), sequence
alignment score = 641.2
RMSD between 106 pruned atom pairs is 0.952 angstroms; (across all 145 pairs:
4.335)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.12), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.983 angstroms; (across all 145 pairs:
4.326)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.13), sequence
alignment score = 641.2
RMSD between 101 pruned atom pairs is 0.902 angstroms; (across all 145 pairs:
4.394)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.14), sequence
alignment score = 665.2
RMSD between 103 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.465)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.15), sequence
alignment score = 640.6
RMSD between 105 pruned atom pairs is 1.003 angstroms; (across all 145 pairs:
4.384)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.16), sequence
alignment score = 672.4
RMSD between 106 pruned atom pairs is 0.999 angstroms; (across all 145 pairs:
4.393)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.17), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.282)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.18), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 1.033 angstroms; (across all 145 pairs:
4.286)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.19), sequence
alignment score = 655.6
RMSD between 105 pruned atom pairs is 0.909 angstroms; (across all 145 pairs:
4.298)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.20), sequence
alignment score = 662.2
RMSD between 105 pruned atom pairs is 0.926 angstroms; (across all 145 pairs:
4.324)
> show #1.1 models
> hide #1.1 models
> show #!2 models
> show #!3 models
> show #!4 models
> ltut
> open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html
Opened https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
modeling.html
> color #5 light gray
> close #5.2-end
> hide #5/A atoms
> label /C height 1
> hide #5/C cartoons
> show #5/C atoms
> label /C height 1
> close #5
> open pdb:2KID
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A
5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A | Sortase |
Q9S446_STAAU
5.1/C 5.2/C 5.3/C 5.4/C 5.5/C 5.6/C 5.7/C 5.8/C 5.9/C 5.10/C 5.11/C 5.12/C
5.13/C 5.14/C 5.15/C 5.16/C 5.17/C 5.18/C 5.19/C 5.20/C | (PHQ)LPA(B27)
peptide |
> matchmaker #5/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.1), sequence
alignment score = 644.2
RMSD between 104 pruned atom pairs is 0.991 angstroms; (across all 145 pairs:
4.403)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.2), sequence
alignment score = 665.2
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.228)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.3), sequence
alignment score = 672.4
RMSD between 105 pruned atom pairs is 0.959 angstroms; (across all 145 pairs:
4.361)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.4), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.342)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.5), sequence
alignment score = 662.2
RMSD between 107 pruned atom pairs is 0.965 angstroms; (across all 145 pairs:
4.238)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.6), sequence
alignment score = 651.4
RMSD between 109 pruned atom pairs is 0.974 angstroms; (across all 145 pairs:
4.293)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.7), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.968 angstroms; (across all 145 pairs:
4.330)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.8), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
4.344)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.9), sequence
alignment score = 669.4
RMSD between 104 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.316)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.10), sequence
alignment score = 679
RMSD between 108 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.261)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.11), sequence
alignment score = 641.2
RMSD between 106 pruned atom pairs is 0.952 angstroms; (across all 145 pairs:
4.335)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.12), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.983 angstroms; (across all 145 pairs:
4.326)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.13), sequence
alignment score = 641.2
RMSD between 101 pruned atom pairs is 0.902 angstroms; (across all 145 pairs:
4.394)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.14), sequence
alignment score = 665.2
RMSD between 103 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.465)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.15), sequence
alignment score = 640.6
RMSD between 105 pruned atom pairs is 1.003 angstroms; (across all 145 pairs:
4.384)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.16), sequence
alignment score = 672.4
RMSD between 106 pruned atom pairs is 0.999 angstroms; (across all 145 pairs:
4.393)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.17), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.282)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.18), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 1.033 angstroms; (across all 145 pairs:
4.286)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.19), sequence
alignment score = 655.6
RMSD between 105 pruned atom pairs is 0.909 angstroms; (across all 145 pairs:
4.298)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.20), sequence
alignment score = 662.2
RMSD between 105 pruned atom pairs is 0.926 angstroms; (across all 145 pairs:
4.324)
> color #5 light gray target c
> close #5.2-end
> hide #5/A atoms
> hide #5/C cartoons
> show #5/C atoms
> hide #5/A
> close #5
> open pdb:2KID
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A
5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A | Sortase |
Q9S446_STAAU
5.1/C 5.2/C 5.3/C 5.4/C 5.5/C 5.6/C 5.7/C 5.8/C 5.9/C 5.10/C 5.11/C 5.12/C
5.13/C 5.14/C 5.15/C 5.16/C 5.17/C 5.18/C 5.19/C 5.20/C | (PHQ)LPA(B27)
peptide |
> matchmaker #5/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.1), sequence
alignment score = 644.2
RMSD between 104 pruned atom pairs is 0.991 angstroms; (across all 145 pairs:
4.403)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.2), sequence
alignment score = 665.2
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.228)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.3), sequence
alignment score = 672.4
RMSD between 105 pruned atom pairs is 0.959 angstroms; (across all 145 pairs:
4.361)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.4), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.342)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.5), sequence
alignment score = 662.2
RMSD between 107 pruned atom pairs is 0.965 angstroms; (across all 145 pairs:
4.238)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.6), sequence
alignment score = 651.4
RMSD between 109 pruned atom pairs is 0.974 angstroms; (across all 145 pairs:
4.293)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.7), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.968 angstroms; (across all 145 pairs:
4.330)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.8), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
4.344)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.9), sequence
alignment score = 669.4
RMSD between 104 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.316)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.10), sequence
alignment score = 679
RMSD between 108 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.261)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.11), sequence
alignment score = 641.2
RMSD between 106 pruned atom pairs is 0.952 angstroms; (across all 145 pairs:
4.335)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.12), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.983 angstroms; (across all 145 pairs:
4.326)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.13), sequence
alignment score = 641.2
RMSD between 101 pruned atom pairs is 0.902 angstroms; (across all 145 pairs:
4.394)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.14), sequence
alignment score = 665.2
RMSD between 103 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.465)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.15), sequence
alignment score = 640.6
RMSD between 105 pruned atom pairs is 1.003 angstroms; (across all 145 pairs:
4.384)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.16), sequence
alignment score = 672.4
RMSD between 106 pruned atom pairs is 0.999 angstroms; (across all 145 pairs:
4.393)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.17), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.282)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.18), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 1.033 angstroms; (across all 145 pairs:
4.286)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.19), sequence
alignment score = 655.6
RMSD between 105 pruned atom pairs is 0.909 angstroms; (across all 145 pairs:
4.298)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.20), sequence
alignment score = 662.2
RMSD between 105 pruned atom pairs is 0.926 angstroms; (across all 145 pairs:
4.324)
> color #5 light gray target c
> close #5.2-end
> hide #5/A
> hide #5/C target c
> hide #5/A
> hide #5/C target c
> show #5/C
> hide H
> label /C height 1
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #1.1 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> show #5/C
> close #5
> open pdb:2KID
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A
5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A | Sortase |
Q9S446_STAAU
5.1/C 5.2/C 5.3/C 5.4/C 5.5/C 5.6/C 5.7/C 5.8/C 5.9/C 5.10/C 5.11/C 5.12/C
5.13/C 5.14/C 5.15/C 5.16/C 5.17/C 5.18/C 5.19/C 5.20/C | (PHQ)LPA(B27)
peptide |
> matchmaker #5/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.1), sequence
alignment score = 644.2
RMSD between 104 pruned atom pairs is 0.991 angstroms; (across all 145 pairs:
4.403)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.2), sequence
alignment score = 665.2
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.228)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.3), sequence
alignment score = 672.4
RMSD between 105 pruned atom pairs is 0.959 angstroms; (across all 145 pairs:
4.361)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.4), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.342)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.5), sequence
alignment score = 662.2
RMSD between 107 pruned atom pairs is 0.965 angstroms; (across all 145 pairs:
4.238)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.6), sequence
alignment score = 651.4
RMSD between 109 pruned atom pairs is 0.974 angstroms; (across all 145 pairs:
4.293)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.7), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.968 angstroms; (across all 145 pairs:
4.330)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.8), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
4.344)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.9), sequence
alignment score = 669.4
RMSD between 104 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.316)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.10), sequence
alignment score = 679
RMSD between 108 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.261)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.11), sequence
alignment score = 641.2
RMSD between 106 pruned atom pairs is 0.952 angstroms; (across all 145 pairs:
4.335)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.12), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.983 angstroms; (across all 145 pairs:
4.326)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.13), sequence
alignment score = 641.2
RMSD between 101 pruned atom pairs is 0.902 angstroms; (across all 145 pairs:
4.394)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.14), sequence
alignment score = 665.2
RMSD between 103 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.465)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.15), sequence
alignment score = 640.6
RMSD between 105 pruned atom pairs is 1.003 angstroms; (across all 145 pairs:
4.384)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.16), sequence
alignment score = 672.4
RMSD between 106 pruned atom pairs is 0.999 angstroms; (across all 145 pairs:
4.393)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.17), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.282)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.18), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 1.033 angstroms; (across all 145 pairs:
4.286)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.19), sequence
alignment score = 655.6
RMSD between 105 pruned atom pairs is 0.909 angstroms; (across all 145 pairs:
4.298)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.20), sequence
alignment score = 662.2
RMSD between 105 pruned atom pairs is 0.926 angstroms; (across all 145 pairs:
4.324)
> color #5 light gray
> close #5.2-end
> show #5/C & ~H
> hide #5/C target c
> label /C height 1
> close #5
> open pdb:2KID
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A
5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A | Sortase |
Q9S446_STAAU
5.1/C 5.2/C 5.3/C 5.4/C 5.5/C 5.6/C 5.7/C 5.8/C 5.9/C 5.10/C 5.11/C 5.12/C
5.13/C 5.14/C 5.15/C 5.16/C 5.17/C 5.18/C 5.19/C 5.20/C | (PHQ)LPA(B27)
peptide |
> matchmaker #5/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.1), sequence
alignment score = 644.2
RMSD between 104 pruned atom pairs is 0.991 angstroms; (across all 145 pairs:
4.403)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.2), sequence
alignment score = 665.2
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.228)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.3), sequence
alignment score = 672.4
RMSD between 105 pruned atom pairs is 0.959 angstroms; (across all 145 pairs:
4.361)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.4), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.342)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.5), sequence
alignment score = 662.2
RMSD between 107 pruned atom pairs is 0.965 angstroms; (across all 145 pairs:
4.238)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.6), sequence
alignment score = 651.4
RMSD between 109 pruned atom pairs is 0.974 angstroms; (across all 145 pairs:
4.293)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.7), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.968 angstroms; (across all 145 pairs:
4.330)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.8), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
4.344)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.9), sequence
alignment score = 669.4
RMSD between 104 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.316)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.10), sequence
alignment score = 679
RMSD between 108 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.261)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.11), sequence
alignment score = 641.2
RMSD between 106 pruned atom pairs is 0.952 angstroms; (across all 145 pairs:
4.335)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.12), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.983 angstroms; (across all 145 pairs:
4.326)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.13), sequence
alignment score = 641.2
RMSD between 101 pruned atom pairs is 0.902 angstroms; (across all 145 pairs:
4.394)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.14), sequence
alignment score = 665.2
RMSD between 103 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.465)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.15), sequence
alignment score = 640.6
RMSD between 105 pruned atom pairs is 1.003 angstroms; (across all 145 pairs:
4.384)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.16), sequence
alignment score = 672.4
RMSD between 106 pruned atom pairs is 0.999 angstroms; (across all 145 pairs:
4.393)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.17), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.282)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.18), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 1.033 angstroms; (across all 145 pairs:
4.286)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.19), sequence
alignment score = 655.6
RMSD between 105 pruned atom pairs is 0.909 angstroms; (across all 145 pairs:
4.298)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.20), sequence
alignment score = 662.2
RMSD between 105 pruned atom pairs is 0.926 angstroms; (across all 145 pairs:
4.324)
> color #5 & C light gray
> close #5.2-end
> hide #5/A
> hide #5/C target c
> show #5/C & ~H
> label /C height 1
> color /C light gray
> hide models
> show #1.2,5 models
> hide models
> show #1.2,#5 models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide models
> show #1.2 #5 models
> hide models
> show #4,5 models
> color ligand light green
> label ligand color light green
> color ligand red
> label ligand height 1 color red
> color /C gold
> label /C height 1 color gold
> color ligand lime
> label delete
> ribbon ligand
> ribbon /C
> ~ribbon ligand
> close #4
> open pdb:1T2W
Summary of feedback from opening 1T2W fetched from pdb
---
warnings | Unknown polymer entity '2' near line 4355
Unknown polymer entity '3' near line 4363
Unknown polymer entity '4' near line 4370
Unknown polymer entity '5' near line 4379
Unknown polymer entity '6' near line 4386
Atom OXT is not in the residue template for GLY /A:335
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
1t2w title:
Crystal Structure of Sortase A in Complex with a LPETG peptide [more info...]
Chain information for 1t2w #4
---
Chain | Description
A B C | sortase
1t2w mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| software_defined_assembly
> matchmaker #4/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 1t2w, chain A (#4), sequence alignment
score = 715.3
RMSD between 134 pruned atom pairs is 0.410 angstroms; (across all 145 pairs:
1.687)
> delete #4/B,C
> hide #4/A & ~ligand
> color #5 gold
> show #!1 models
> show #1.1 models
> close #5
> open pdb:2KID
2kid title:
Solution Structure of the S. Aureus Sortase A-substrate Complex [more info...]
Chain information for 2kid
---
Chain | Description | UniProt
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A
5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A | Sortase |
Q9S446_STAAU
5.1/C 5.2/C 5.3/C 5.4/C 5.5/C 5.6/C 5.7/C 5.8/C 5.9/C 5.10/C 5.11/C 5.12/C
5.13/C 5.14/C 5.15/C 5.16/C 5.17/C 5.18/C 5.19/C 5.20/C | (PHQ)LPA(B27)
peptide |
> matchmaker #5/A to #1.1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.1), sequence
alignment score = 644.2
RMSD between 104 pruned atom pairs is 0.991 angstroms; (across all 145 pairs:
4.403)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.2), sequence
alignment score = 665.2
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.228)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.3), sequence
alignment score = 672.4
RMSD between 105 pruned atom pairs is 0.959 angstroms; (across all 145 pairs:
4.361)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.4), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 0.955 angstroms; (across all 145 pairs:
4.342)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.5), sequence
alignment score = 662.2
RMSD between 107 pruned atom pairs is 0.965 angstroms; (across all 145 pairs:
4.238)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.6), sequence
alignment score = 651.4
RMSD between 109 pruned atom pairs is 0.974 angstroms; (across all 145 pairs:
4.293)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.7), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.968 angstroms; (across all 145 pairs:
4.330)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.8), sequence
alignment score = 662.8
RMSD between 105 pruned atom pairs is 1.024 angstroms; (across all 145 pairs:
4.344)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.9), sequence
alignment score = 669.4
RMSD between 104 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.316)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.10), sequence
alignment score = 679
RMSD between 108 pruned atom pairs is 0.939 angstroms; (across all 145 pairs:
4.261)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.11), sequence
alignment score = 641.2
RMSD between 106 pruned atom pairs is 0.952 angstroms; (across all 145 pairs:
4.335)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.12), sequence
alignment score = 641.2
RMSD between 104 pruned atom pairs is 0.983 angstroms; (across all 145 pairs:
4.326)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.13), sequence
alignment score = 641.2
RMSD between 101 pruned atom pairs is 0.902 angstroms; (across all 145 pairs:
4.394)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.14), sequence
alignment score = 665.2
RMSD between 103 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.465)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.15), sequence
alignment score = 640.6
RMSD between 105 pruned atom pairs is 1.003 angstroms; (across all 145 pairs:
4.384)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.16), sequence
alignment score = 672.4
RMSD between 106 pruned atom pairs is 0.999 angstroms; (across all 145 pairs:
4.393)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.17), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 0.966 angstroms; (across all 145 pairs:
4.282)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.18), sequence
alignment score = 640.6
RMSD between 106 pruned atom pairs is 1.033 angstroms; (across all 145 pairs:
4.286)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.19), sequence
alignment score = 655.6
RMSD between 105 pruned atom pairs is 0.909 angstroms; (across all 145 pairs:
4.298)
Matchmaker 1t2p A, chain A (#1.1) with 2kid, chain A (#5.20), sequence
alignment score = 662.2
RMSD between 105 pruned atom pairs is 0.926 angstroms; (across all 145 pairs:
4.324)
> close #5.2-end
> hide #5/A
> hide #5/C target c
[Repeated 1 time(s)]
> show #5/C & ~H
> show #!2 models
> show #!3 models
> hide #!4 models
> show #!1.2 models
> show #1.2.1 models
> hide #!2 models
> show #!2 models
> hide #3
> alphafold match #1/b
Traceback (most recent call last):
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute
cmd.run(cmd_text)
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/match.py", line 39, in alphafold_match
search_seq_models = _fetch_by_sequence(session, search_seqs,
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/match.py", line 98, in _fetch_by_sequence
_alphafold_models(session, sequences, seq_uids,
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/match.py", line 126, in _alphafold_models
models, status = alphafold_fetch(session, uid.uniprot_id,
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/fetch.py", line 37, in alphafold_fetch
_set_alphafold_model_attributes(models, uniprot_id, uniprot_name)
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alphafold/match.py", line 167, in
_set_alphafold_model_attributes
AtomicStructure.register_attr(model.session, "alphafold", "AlphaFold",
attr_type=bool)
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 68, in register_attr
cls._attr_registration.register(session, attr_name, registerer, default_value,
(attr_type, can_return_none))
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 95, in register
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"
chimerax.core.attributes.RegistrationConflict: Registration of attr
'alphafold' with AtomicStructure by AlphaFold conflicts with previous
registration by AlphaFold
chimerax.core.attributes.RegistrationConflict: Registration of attr
'alphafold' with AtomicStructure by AlphaFold conflicts with previous
registration by AlphaFold
File
"/Users/meng/Desktop/ChimeraX-1.3-rc2021.10.26.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 95, in register
raise RegistrationConflict("Registration of attr '%s' with %s by %s conflicts
with previous"
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-14.7.20
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 428.40.10.0.0
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1519)
Kernel Version: Darwin 19.6.0
Time since boot: 9:52
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.30.2
ChimeraX-AtomicLibrary: 4.1.5
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3rc202110261847
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.2
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.4
ChimeraX-ModelPanel: 1.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.4
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.5
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.6
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.10.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.0
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.21
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.1
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
example session from 1.4 daily build with alphafold results (sorry kinda big, has lots of other models too)