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'*], self.residues['*668: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