[modeller_usage] a question about add hidrogen

[Atila Iamarino <>]

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?

--
Atila Iamarino
L.E.M.B. - Laboratory of Molecular Evolution and Bioinformatics
Av. Prof. Lineu Prestes, 1734 - USP (University of São Paulo) - ICB
Zip: 05508-000 Phone: +55 11 30917290 / +55 11 30918453