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[modeller_usage] Problem applying two different restrictions ...(solved)

Dear Dr. Arvind and Dr. Webb

Thank you very much for your help. The problem as you point out was the
lacking of the cystein's chain identification.

Below I paste the corrected script (in case other people look up this kind of errors in the list):

 # Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class MyModel(automodel):
    def special_patches(self, aln):
        # A disulfide between residues 345 and 668:
        self.patch(residue_type='DISU', residues=(self.residues['345:A'],

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

# Read in HETATM records from template PDBs
env.io.hetatm = True

a = MyModel(env,
            alnfile  = 'alignment.ali',  # alignment filename
            knowns   = ('2ioaB_amidase', '2vobB', '2ioaB_sinthetase'),  # codes of the templates
            sequence = 'tcruzi')              # code of the target
a.starting_model= 3                 # index of the first model
a.ending_model  = 3                 # index of the last model
                                        # (determines how many models to calculate)
a.make()                            # do the actual homology modeling

Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221