Hi! I tried to generate a theoretical alpha-helix with the example from Modeller's Manual, but just don't work, because rasmol not identified as helix (my sequence is longer than example). I use more iterations ( 1x10^9) and get a better result but is not enough. Somebody know a better way to generate a perfect alpha helix?? I really need a theoretical helix for my work, please help me.
This is the example:
# 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('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 = conjugate_gradients() cg.optimize(allatoms, max_iterations=100) m.write(file='alpha-helix.pdb')
P.D. I apologize for my English, i hope you understand me.
Thanks!