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 filenameknowns = ’templateA’, # codes of the templatessequence = ’Query’) # code of the targeta.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----------------------------------------------------------------------------------------- Dr. Pawan Kumar GuptaResearch Scientist CNS, Active Compound Library Latvian Institute of Organic SynthesisRiga, Latvia Office: +371-22374710 Website: https://sites.google.com/site/pawanpharma79/
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