Hi.

I am trying to model a protein that has a C-terminal region without template match. However, the secondary structure prediction strongly suggests that part of this terminal region forms a beta-strand (residues 125 to 128). I am trying to generate an antiparallel beta sheet from this terminal segment, bonding with a pre-existing beta strand (residues 79-82). However, the generated model does not answer this command, being equal to the model generated without the command.

Could you point out what I am doing wrong?

Below are the script file.

Thanks in advance.

# Homology modeling with multiple templates from modeller import *              # Load standard Modeller classes from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output env = environ()  # create a new MODELLER environment to build this model in env.io.water = True

# Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class MyModel(automodel):     def special_patches(self, aln):         rsr = self.restraints         at = self.atoms

#       A disulfide between residues:         self.patch(residue_type='DISU', residues=(self.residues['9'], self.residues['30']))         self.patch(residue_type='DISU', residues=(self.residues['53'], self.residues['74']))

#       Two beta-strands:         rsr.add(secondary_structure.strand(self.residue_range('79:', '82:')))         rsr.add(secondary_structure.strand(self.residue_range('125:', '128:'))) #       An anti-parallel sheet composed of the two strands:         rsr.add(secondary_structure.sheet(at['N:79'], at['O:128'],                                           sheet_h_bonds=-4))

a = MyModel(env, alnfile = 'Maycon3-1template.ali', knowns = '1template', sequence = 'Maycon3', assess_methods=(assess.DOPE, assess.GA341))

a.starting_model = 1 a.ending_model = 100 a.make()