On 9 March 2011 14:59, Claudia Scotti <claudiascotti@hotmail.com> wrote:

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.alpha(self.residue_range('39:', '45:')))
# Two beta-strands:
# rsr.add(secondary_structure.strand(self.residue_range('1:', '5:')))
# rsr.add(secondary_structure.strand(self.residue_range('19:', '26:')))
# rsr.add(secondary_structure.strand(self.residue_range('33:', '35:')))
# rsr.add(secondary_structure.strand(self.residue_range('55:', '58:')))
rsr.add(secondary_structure.strand(self.residue_range('68:', '72:')))
# An anti-parallel sheet composed of the two strands:
# rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'],
# sheet_h_bonds=-5))
# Use the following instead for a *parallel* sheet:
# rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'],
# 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=physical.xy_distance,
# feature=features.distance(at['CA:35'],
# 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

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