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!
Hi,
I asked similar question some time ago and the answer was: https://salilab.org/archives/modeller_usage/2013/msg00118.html
You can use instead UCSF Chimera (Tools -> Structure Editing -> Build Structure: check "peptide sequence" checkbox, input your sequence, then click Apply and then you have option to force ideal alpha helix angles).
Cheers, Jan
On 04/02/2014 04:19 PM, Francisco garcia wrote: > 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! > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
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Francisco garcia -
Jan Kosinski