dear modeller, I wanted to restrain secondary structure in the target sequenc and I've used the following command (see bottom). The outcoming structure included the wanted alpha-helices but the structure didn't contain the anti-parallel sheet. What did I do wrong?

renée vancraenenbroeck renée.vancraenenbroeck@student.kuleuven.ac.be

from modeller.automodel import *

# Redefine the special_restraints routine to include the secondary # structure restraints (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # An alpha-helix: rsr.make(aln, restraint_type='ALPHA', residue_ids= ('133', '146'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids=('69', '83'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids= ('164', '177'), spline_on_site=False) rsr.make(aln, restraint_type='ALPHA', residue_ids= ('96', '113'), spline_on_site=False) # Two strands: rsr.make(aln, restraint_type='STRAND', residue_ids= ('44', '54'), spline_on_site=False) rsr.make(aln, restraint_type='STRAND', residue_ids= ('56', '66'), spline_on_site=False) # An anti-parallel sheet: rsr.make(aln, restraint_type='SHEET', atom_ids= ('N:44', 'O:66'), sheet_h_bonds=-5, spline_on_site=False)

log.verbose() env = environ()

a = mymodel(env, alnfile='Lrrk2-mult5.ali', knowns=('2aedA','1byuA'), sequence='Lrrk2roc') a.make()