[modeller_usage] Problem applying two different restrictions ...(solved)
To:
Subject: [modeller_usage] Problem applying two different restrictions ...(solved)
From: Sergio Garay <>
Date: Fri, 6 Mar 2009 03:49:20 -0500
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
-- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221