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.
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On 10/25/10 3:30 PM, Orhan Ertughrul wrote: > 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 restraints are consistent with an alpha-helical structure but they are also consistent with other structures (they are quite loose). They are designed really just to "encourage" a structure to adopt an alpha-helical-like conformation but will typically not force a perfect alpha helix.
Ben Webb, Modeller Caretaker
It is not exactly what you asked but this may do the trick:
Look for a program named ribosome - it makes regular protein structures given the sequence.
At 09:15 AM 10/26/2010, Modeller Caretaker wrote: >On 10/25/10 3:30 PM, Orhan Ertughrul wrote: > > Iâve been using a standard script to build an alpha helix from an > > alanine chain. Modeller generates the restrained structure but it isnât > > alpha-helical when viewed in PYMOL.
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================
You can also do the same thing as Mensur said in Chimera (you have the advantage of the GUI there) using Tools->Structure Editing->Build Structure. You may also modify a fragment of your model to adapt to an alpha-helical conformation although that requires more effort. I'm not sure about the limitations of Chimera in comparison with Ribosome, I have never used the latter.
On 26 October 2010 18:39, Mensur Dlakic mdlakic@montana.edu wrote:
> It is not exactly what you asked but this may do the trick: > > http://www.roselab.jhu.edu/ > > Look for a program named ribosome - it makes regular protein structures > given the sequence. > > At 09:15 AM 10/26/2010, Modeller Caretaker wrote: > >On 10/25/10 3:30 PM, Orhan Ertughrul wrote: > > > 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. > > ========================================================================== > | Mensur Dlakic, PhD | Tel: (406) 994-6576 | > | Department of Microbiology | Fax: (406) 994-4926 | > | Montana State University | | > | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | > | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | > ========================================================================== > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
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Mensur Dlakic -
Modeller Caretaker -
Orhan Ertughrul -
Thomas Evangelidis