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. But will you pass me the script lines which aligns structures at 1,2,3,4Angstroms. My another doubt is that how the considered structures are considered all together for each of these distance cutoffs. Is this like nC2 combination based structural alignment satisfaction of restraint matrix generated. Show me where these 1,2,3,4 Angstroms are available in salign_iterative. I couldn't find them.
Thanks, Ashish
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
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Ashish Runthala -
Modeller Caretaker