On 1/20/11 7:11 PM, Ashish Runthala wrote: > 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.
Ben Webb, Modeller Caretaker