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