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 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'] a = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('template','template2'), # codes of the templates sequence = 'target') # code of the target a.starting_model= 1 # index of the first model a.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 Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : |