Dear users,
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?
Thanks in advance,
Giacomo Bastianelli
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
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
Giacomo Bastianelli wrote: > I tried as you suggested, however I cannot have the > cyclic form of my protein.
That doesn't give me much information to go on, but if you send me your input files, I can take a look.
> I tried also writing differently the IDs ('1' or '1:' or '1:A')..
The example I sent you works, although obviously if your C terminus is not at residue number 54, you'll have to change that. The N terminus should always be 1, unless you have done something very unusual.
Ben Webb, Modeller Caretaker
participants (2)
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Giacomo Bastianelli -
Modeller Caretaker