[modeller_usage] problem with modelling a non-template helix

["Renée Vancraenenbroeck" <>]

dear modellers,
I've come to the problem where I have to elongate a helix but the 
template is absent, I've tried to restrain it into a helixconformation 
using the following script wich I found in the archive, however it 
doesn't seem to make any difference. What am I doing wrong?

renée vancraenenbroeck

 

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', '139'),
                 spline_on_site=False)
        

# This is as usual:
log.verbose()
env = environ()
a = automodel(env, alnfile='Lrrk2-mult5.ali',
              knowns=('2aedA','1byuA'), sequence='Lrrk2roc')
a.starting_model = 1
a.ending_model = 5
a.make()