Hi!
I'm using MODELLER to build a homology model of my protein. In my first try, I create a model without any restraint, and then I compared the secondary structure of this model (Using STRIDE and VMD) with the secondary structure predict by PSIPRED webserver. For the first 26 residues, I have these predictions:
PSIPRED: CHHHHHHHHHHHHHHHHHHHHHHHHC
Homology model: CCCCCCCCCCCCHHHHHHHHHHHHHC
My idea is restraint the region where the predictions are coincidences (13:A to 26:A) and applying restraints to force an alpha Helix structure between residues 3 and 11. I didn't include the residues 2 and 12 in order to give some flexibility to MODELLER to connect the restraint to the remainder of the protein (see below).
from modeller import *
from modeller.automodel import *
import sys
log.verbose()
env = environ()
class MyModel(automodel):
def select_atoms(self):
return selection(self.residue_range('13:A', '26:A'))
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
# Define an alpha helix
rsr.add(secondary_structure.alpha(self.residue_range('3:A', '11:A')))
But, when I look this region on VMD, I don't have a Helix between residues 2 to 12. I don't know, what I'm doing wrong. Is a better approach to restraint as Helix from 2 to 26? Should I keep some regions without optimization during the restraint protocol?
Thank in advance,
Fred