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Re: [modeller_usage] cyclic peptide modeling

Dear Ben Webb,

I tried as you suggested, however I cannot have the
cyclic form of my protein.
I tried also writing differently the IDs ('1' or '1:' or '1:A')..

Giacomo

Modeller Caretaker wrote:

Giacomo Bastianelli wrote:

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