Hi All,

 

I’ve been using a standard script to build an alpha helix from an alanine chain. Modeller generates the restrained structure but it isn’t alpha-helical when viewed in PYMOL. The code I’m using is below:

 

# Example for model.build_sequence(), secondary_structure.alpha()

 

from modeller import *

from modeller.optimizers import conjugate_gradients

 

# Set up environment

e = environ()

e.libs.topology.read('${LIB}/top_heav.lib')

e.libs.parameters.read('${LIB}/par.lib')

 

# Build an extended chain model from primary sequence, and write it out

m = model(e)

m.build_sequence('AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA')

m.write(file='extended-chain.pdb')

 

# Make stereochemical restraints on all atoms

allatoms = selection(m)

m.restraints.make(allatoms, restraint_type='STEREO', spline_on_site=False)

 

# Constrain all residues to be alpha-helical

# (Could also use m.residue_range() rather than m.residues here.)

m.restraints.add(secondary_structure.alpha(m.residue_range('1:','36:')))

 

# Get an optimized structure with CG, and write it out

cg = conjugate_gradients()

cg.optimize(allatoms, max_iterations=100)

m.write(file='alpha-helix.pdb')

 

I figure I must be doing something wrong but I can’t see it. Any pointers would be much appreciated.

 

Thanks!

 

Orhan.