Hi there,
I have this py file to include disulfide bonds:
from modeller import * from modeller.automodel import *
class mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['85:B'],self.residues['111:B'])) log.verbose() env = environ()
a = mymodel(env, alnfile = 'multiple.ali', knowns = ('1', '2'), sequence = '3', assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1 a.ending_model = 10
a.make()
# Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs)
# Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key]))
# Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key])
I want to include hidrogens to the protein and a substrate that's on one of the templates to make a simulated annealing. And by the way, modeller does not make simmulated annealing wrigth?