Hi,
It should be enough to replace the region with dashes "-" and have a chain break ("/") either right before or after the dashes to make sure modeller does not try to pull the flanking residues together. Something like this:
Template AAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAA Target BBBBBBBBBBBB/----------BBBBBBBBBBBBBBBBB
Best,
Roberto
-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/
> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On > Behalf Of Gowthaman R > Sent: Thursday, December 12, 2002 2:50 PM > To: modeller_usage@salilab.org > Cc: Bozidar Yerkovich > Subject: leaving gaps in non aligned regions > > > > hello modellers, > i am trying to model some proteins. but my protein has some region > (internal) (15-20 amino acids) which does not have any > corresponding region in the template sequence. i DO NOT > want to model that region and in my final (3D) strucuture i > want to have a gap in the corresponding internal region. > other wise that region forms a loop or extended region ( > makes the structre ugly ??). i wish to know how my alignement > file should look like.... > > > i tried following and did not solve the problem > 1) putting " X " for the amino acids for which i dont want > the 3D structure to be made > > 2) puting " - " for the same... > > waiting for ur reply > > gowthaman > Phd Student > ICGEB, > India. > >