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Dear All, Please, I cannot model a beta strand (predicted as such by PSI PRED) in a protein model, even adding further restraints. I think this depends on the fact that this region is not structured in the templates. Please, any suggestions (see .py below)? Many thanks. Claudia ------- # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class 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'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # unpick('1:', '73:') # condense('1:', '73:') # Add some restraints from a file: # rsr.append(file='my_rsrs1.rsr' # Residues 49 through 55 should be an alpha helix: rsr.add(secondary_structure. # Two beta-strands: # rsr.add(secondary_structure. # rsr.add(secondary_structure. # rsr.add(secondary_structure. # rsr.add(secondary_structure. rsr.add(secondary_structure. # An anti-parallel sheet composed of the two strands: # rsr.add(secondary_structure. # sheet_h_bonds=-5)) # Use the following instead for a *parallel* sheet: # rsr.add(secondary_structure. # sheet_h_bonds=5)) # Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1) # Use a harmonic potential and X-Y distance group. # rsr.add(forms.gaussian(group= # feature=features.distance(at[' # at['CA:40']), # mean=10.0, stdev=0.1)) a = MyModel(env, alnfile = 'Alignment2.ali', # alignment filename knowns = ('pco','Tas','gen','Rap'), # codes of the templates sequence = 'sALK1') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling -- Claudia Scotti, MD PhD Department of Experimental Medicine University of Pavia Via Ferrata, 1 27100 Pavia Italy Tel. 0382 986335 Facs 0382 986893 Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Via Ferrata, 1 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 |