additional restraints in Modeller - modeller_usage

6 Sep 2013


      Hi Modeller users,
I want to add some additional restraints during homology modelling, but 
it seems to be not working. And I did not found any error complaining  
the restraints.
Here is my script:
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ()
env.io.atom_files_directory = '/home/qinghua/Projects/Tycko/HM'
class MyModel(automodel):
     def special_restraints(self, aln):
         rsr = self.restraints
         at = self.atoms
# CONSTRAINTS ON HISTIDINE 6
         rsr.add(forms.gaussian(group=physical.xy_distance,
feature=features.distance(at['CG:13:B'],at['CG:14:B']),
                                mean=4.00, stdev=0.05))
#        rsr.add(forms.gaussian(group=physical.xy_distance,
# feature=features.distance(at['NE2:14:B'],at['O:13:B']),
#                               mean=3.03, stdev=0.05))
env = environ()
a = automodel(env, alnfile='2LMO-aln.ali',
               knowns='abcdB', sequence='2LMO',
               assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 5
a.make()
This is just a test, I want to make sure that the restraints work here. 
However, I checked the output pdb files, and I found that the distance 
between Atom CG and CG is larger
than 4 angstrom.
Could someone give me some suggestion for it? Thanks very much!
All the best,
Qinghua