[modeller_usage] modeller

["Renée Vancraenenbroeck" <>]

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  
rené


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()