[modeller_usage] additional restraints in Modeller

[fantasticqhl <>]

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