# comparative modeling

from modeller.automodel import * # Load the automodel class

class mymodel(automodel):

def special_restraints(self, aln):

rsr = self.restraints

rsr.make(aln, restraint_type='STRAND',residue_ids=('171','172'))

log.very_verbose() # request verbose output

env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files

env.io.atom_files_directory = ['.', '../atom_files']

a = automodel(env,

alnfile = 'alignment.ali', # alignment filename

knowns = ('template','template2'), # codes of the templates

sequence = 'target') # code of the target

a.starting_model= 1 # index of the first model

a.ending_model = 5 # index of the last model

# (determines how many models to calculate)

a.make() # do the actual homology modelling

I have a doubt regarding this script as didn't get the desired restraints in the modelled protein.The residue_ids that we have to provide should be a range as my loop regions exists between two ends of beta strands i.e. 171 and 175 amino acid .