Dear Members
I
am trying to build a model using constraint in secondary structure. I
tried to compile the script using different key word for secondary
structure constraints, I edited the script and put the constraints in
script with the help of manual as given below, it is not executed and
showing error .....could anybody help me out where is the problem in the
script and how to run this python script for building the model, I do
not know python programming, may be some python commands are not
compatible to any one or some commands in script soit is not
executing....please sort it out................... I will be highly
thankful to you
thanks in advance
_______________input script for model buidling----------------------------------------------------
# examples/automodel/model-addrsr.py
# Addition of restraints to the default ones
from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
env = environ()
# 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
# Add some restraints from a file:
# rsr.append(file=’my_rsrs1.rsr’)
# Residues 20 through 30 should be an alpha helix:
rsr.add(secondary_structure.alpha(self.residue_range(’20:’, ’30:’)))
# Two beta-strands:
rsr.add(secondary_structure.strand(self.residue_range(’1:’, ’6:’)))
rsr.add(secondary_structure.strand(self.residue_range(’9:’, ’14:’)))
# 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 = ’alignment.ali’, # alignment filename
knowns = ’templateA’, # codes of the templates
sequence = ’Query’) # 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 homology modeling
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Dr. Pawan Kumar Gupta
Research Scientist
CNS, Active Compound Library
Latvian Institute of Organic Synthesis
Riga, Latvia
Office: +371-22374710
Please do not print the mail unless necessary