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):
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:
# An anti-parallel sheet composed of the two strands:
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