Report sequence identity from MAV

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202108070803 (2021-08-07 08:03:28 UTC)
Description
How do I get the sequence identity when I have an MAV 2 sequence alignment?  I want to know how many pair residues in the sequences have identical amino acid type.

The best I could come up with was "select ::seq_onservation > 0.5 & #1" but this just counts residues with coordinates and I'd like to count all identical residues in the sequence alignment.

Log:
UCSF ChimeraX version: 1.3.dev202108070803 (2021-08-07)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7n98

Summary of feedback from opening 7n98 fetched from pdb  
---  
note | Fetching compressed mmCIF 7n98 from
http://files.rcsb.org/download/7n98.cif  
  
7n98 title:  
Cryo-EM structure of MFSD2A [more info...]  
  
Chain information for 7n98 #1  
---  
Chain | Description | UniProt  
A | Sodium-dependent lysophosphatidylcholine symporter 1 | NLS1_MOUSE  
  

> ui tool show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service16286137368141756948810  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16286137368141756948810  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

> open pdb:4M64

Summary of feedback from opening 4M64 fetched from pdb  
---  
note | Fetching compressed mmCIF 4m64 from
http://files.rcsb.org/download/4m64.cif  
  
4m64 title:  
3D crystal structure of Na+/melibiose symporter of Salmonella typhimurium
[more info...]  
  
Chain information for 4m64 #2  
---  
Chain | Description | UniProt  
A B C D | Melibiose carrier protein | MELB_SALTY  
  
4m64 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #2/A to #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 7n98, chain A (#1) with 4m64, chain A (#2), sequence alignment
score = 511.2  
RMSD between 67 pruned atom pairs is 1.393 angstroms; (across all 426 pairs:
8.065)  
  

> delete #2/B,C,D

> mmaker #2 to #1 showalign 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 7n98, chain A (#1) with 4m64, chain A (#2), sequence alignment
score = 511.2  
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: 7n98 #1/A, 4m64 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 67 pruned atom pairs is 1.393 angstroms; (across all 426 pairs:
8.065)  
  

> select #1

3625 atoms, 3726 bonds, 473 residues, 1 model selected  

> sequence header conservation show

Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  

> select ::seq_conservation > .5

1351 atoms, 1240 bonds, 172 residues, 2 models selected  

> select ::seq_conservation > .5 & #1

678 atoms, 624 bonds, 86 residues, 1 model selected  

> select #1

3625 atoms, 3726 bonds, 473 residues, 1 model selected  




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[pett]

Yet another capability missing from ChimeraX, and another one that requires parameters (sequences involved; what to use as the denominator). If you only have one alignment open then:

session.alignments.alignments[0].seqs

are the sequences of the alignment, and:

seq.characters

is a list of the characters in the sequence. You can go hog wild from there.

[goddard@…]

Thanks for the tips about getting sequence info via Python!  Mostly requesting this as a user feature.  Could even just report the number of identical residues in matchmaker output and the two sequence lengths and I can divide as I wish.

[pett]

"seq id" command and "Percent Identity..." context menu entry.