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