[modeller_usage] Model missing residues in a trimer
Subject: [modeller_usage] Model missing residues in a trimer
From: Panagiotis Kastritis <>
Date: Mon, 26 Oct 2009 19:13:34 +0100
I would like to ask you how is it possible to model missing residues in
a trimer that I have.
All the monomers have missing residues and each chain has numbering from
1 to 100 let's say.
I searched the archive but I haven't found such question.
I can try this one
/from modeller import *
from modeller.automodel import * # Load the automodel class
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
return selection(self.residue_range('133', '135'),
a = MyModel(env, alnfile = 'alignment.ali',
knowns = '1qg8', sequence = '1qg8_fill')
a.ending_model = 1
/but how can I expand it to more than one chain? I would like only to
fill the missing residues, with only local minimization of the structure
and not global.
Is it possible to do it in modeller?
Thank you in advance,