[modeller_usage] Refine part of an existing model

[flavio seixas <>]

Hi Modellers

I generated a 1000 models of a protein using Modeller.
The best one shows 3 residues in disallowed regions of Ramachandram plot.
I want to refine only regions around those 3 residues which are in helical segments.
The script I am using in is not working. 
Unfortunately I am not familiar with pyton script.
The error message and script file are as follow:




  File "model-segment.py", line 35
    a = MyModel(env, inimodel='182.pdb', sequence='Seq-target')
    ^
SyntaxError: invalid syntax

---------------------------------------------------------------------------

from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()

env = environ()

env.io.atom_files_directory = ['.', '../atom_files']

# selected atoms do not feel the neighborhood
env.edat.nonbonded_sel_atoms = 2

env.io.hetatm = True

class MyModel(automodel):
    def select_atoms(self):
        # Select residues (PDB numbering)
        return selection(self.residue_range('72:A', '75:A'),
                        (self.residue_range('165:A', '167:A'),
                        (self.residue_range('199:A', '201:A'))


# Be sure to use 'MyModel' rather than 'automodel' here!
a = MyModel(env, inimodel='182.pdb', sequence='Seq-target')


a.starting_model= 1                # index of the first model
a.ending_model  = 1                # index of the last model
                                   # (determines how many models to calculate)
a.make()                           # do homology modeling



Could someone help me in this regard?
Thanks for any help.

Flavio