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 renee.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', '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()
Renée Vancraenenbroeck wrote: > 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 > renee.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', '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()
Simply replace 'a=automodel' with 'a=mymodel'.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Renée Vancraenenbroeck