from modeller.automodel import *
class mymodel(automodel):
    def special_restraints(self, aln):
        rsr = self.restraints
        for ids in (('OD1:64:A', 'O1L:149:B'),
                    ('NE1:82:A', 'O3B:149:B'),
                    ('OD2:120:A', 'O6A:149:B')):
                    atoms = [self.atoms[i] for i in ids]
                    rsr.add(forms.upper_bound(group=physical.upper_distance,
                      feature=features.distance(*atoms), mean=3.5, stdev=0.1)) 
env = environ()
env.io.hetatm = True
a = mymodel(env, alnfile='aln.pir', knowns=('1lmp'), sequence='seq')
a.starting_model = 1
a.ending_model = 5
a.make()