Make alpha helix: Difference between revisions
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# Example for Model.build_sequence(), secondary_structure.Alpha() | # Example for Model.build_sequence(), secondary_structure.Alpha() | ||
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cg.optimize(allatoms, max_iterations=100) | cg.optimize(allatoms, max_iterations=100) | ||
m.write(file='alpha-helix.pdb') | m.write(file='alpha-helix.pdb') | ||
</ | </syntaxhighlight> | ||
Revision as of 20:33, 16 August 2022
The example below builds a small model from primary sequence alone, and makes it alpha-helical.
# Example for Model.build_sequence(), secondary_structure.Alpha()
from modeller import *
from modeller.optimizers import ConjugateGradients
# 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('GSCASVCGV')
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.residues))
# Get an optimized structure with CG, and write it out
cg = ConjugateGradients()
cg.optimize(allatoms, max_iterations=100)
m.write(file='alpha-helix.pdb')