I checked salign too. It considers penalties on primary sequence and
then moves to the structural alignment of considered structures
before adding target sequence according to generated structural
topology.
This is not how salign functions in general, but this is basically how
the iterative_structural_align() method functions. It uses an
SALIGN-generated sequence alignment as the starting point for a
structural alignment.
But will you pass me the script lines which aligns
structures at 1,2,3,4Angstroms.
You can generate a quality score at any cutoff you desire. Set
output='QUALITY' and rms_cutoff to the desired cutoff. For the
iterative_structural_align() a cutoff of 3.5A is used.