Whenever the SAlign is implemented with a set of templates, it
generates a matrix showing some mutual similarity of templates
(pairwise equivalences), something like this (against the target with
326 residues).
1SMQA 1H0OA
1SMQA 0 168
1H0OA 0 0
If you run with verbose logging, you'll see something like this in the
log file:
Two residues are equivalent when closer than RMS_CUTOFF upon
pairwise least-squares superposition given current alignment.
SALIGN______> Matrix of pairwise equivalences:
1SMQA 1H0OA
1SMQA 0 168
1H0OA 0 0
1. Is 168 showing the count of similar residues, falling within the
specified RMSD threshold?
2. Is this calculation considering LGA algorithm?
As per the log file, it's just the number of residues that are within
RMS_CUTOFF angstroms of each other.