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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. |