On 11/20/2012 07:42 PM, Ashish Runthala wrote: > 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.
Ben Webb, Modeller Caretaker