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. http://www.avast.com