Hi, I am using the following script for restraining the beta strands in my protein (after searching the mailing archives):- # comparative modeling from modeller.automodel import * # Load the automodel class
class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.make(aln, restraint_type='STRAND',residue_ids=('171','172'))log.very_verbose() # request verbose outputenv = environ() # create a new MODELLER environment to build this model in# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('template','template2'), # codes of the templates sequence = 'target') # code of the targeta.starting_model= 1 # index of the first modela.ending_model = 5 # index of the last model# (determines how many models to calculate)a.make() # do the actual homology modelling ------------------------------I have a doubt regarding this script as didn't get the desired restraints in the modelled protein.The residue_ids that we have to provide should be a range as my loop regions exists between two ends of beta strands i.e. 171 and 175 amino acid .
Bharat
Ph.D. Candidate
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Pusan National University
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