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here is the python script for model building:

#model with restrainin sec. structure and optimization after modeling, by MD
from modeller import *
from modeller.automodel import *    # Load the automodel class


# directories for input atom files

class MyModel (automodel):
def special_restraints(self, aln):


#       Residues should be an alpha helix:
rsr.add(secondary_structure.alpha(self.residue_range(’10:’, ’30:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’41:’, ’49:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’54:’, ’59:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’61:’, ’66:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’80:’, ’100:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’104:’, ’107:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’180:’, ’200:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’202:’, ’207:’)))
rsr.add(secondary_structure.alpha(self.residue_range(’210:’, ’219:’)))
#       Residues should be beta-strands:
rsr.add(secondary_structure.strand(self.residue_range(’111:’, ’116:’)))
rsr.add(secondary_structure.strand(self.residue_range(’133:’, ’135:’)))
rsr.add(secondary_structure.strand(self.residue_range(’144:’, ’146:’)))
rsr.add(secondary_structure.strand(self.residue_range(’158:’, ’164:’)))


log.verbose()
env = environ()
env.io.atom_files_directory = ['.', './template_struc']
a = automodel (env,

alnfile  = ’Q99720-3CIA_AA.ali’,     # alignment filename
knowns   = ’3CIA_A’,              # codes of the templates
sequence = ’Q99720’)              # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model  = 10                 # index of the last model

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please help me out ......i am trying last few months for this ..

I will be highly thankful to you.

Regards

PKG