[modeller_usage] Model missing residues in a trimer

[Panagiotis Kastritis <>]

Dear all,

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

log.verbose()
env = environ()

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

class MyModel(automodel):
   def select_atoms(self):
       return selection(self.residue_range('133', '135'),
                        self.residue_range('216', '230'))

a = MyModel(env, alnfile = 'alignment.ali',
           knowns = '1qg8', sequence = '1qg8_fill')
a.starting_model= 1
a.ending_model  = 1

a.make()

/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,

Panagiotis