Re: [modeller_usage] cyclic peptide modeling

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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