I am modelling mutations and insertions of an
original cyclic peptide sequence.
However, when I run the modeling, I always
loose my cyclization.
Does modeller recognize cyclic peptides for the
modeling?
By default, Modeller assumes a simple polypeptide chain, and does not
connect the N and C terminii. To force a cyclic model, you will need to
explicitly link the terminii, using a script similar to those for
questions 3 and 13 in the FAQ, below (replace 54 and 1 with the residue
IDs of your C and N terminii respectively):
from modeller.automodel import *
env = environ()
# Disable default NTER and CTER patching
env.patch_default=False
class mymodel(automodel):
def special_patches(self, aln):
# Link between residues 54 and 1 to make chain cyclic:
self.patch(residue_type='LINK', residue_ids=('54:', '1:'))
a = mymodel(env, ... (etc.)
a.make()
Ben Webb, Modeller Caretaker
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