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.



avast! Antivirus: Outbound message clean.

Virus Database (VPS): 101025-1, 25/10/2010
Tested on: 25/10/2010 23:30:07
avast! - copyright (c) 1988-2010 AVAST Software.