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