Have you tried to leave this region of your target sequence unaligned? Modeller uses restraints derived from the templates and since this region is a coil in your templates the coil conformation will prevail over the strand. Also manually added secondary structure restraints tend to be weak. In my experience strands (especially those within sheets) that are coil-like in the crude homology model acquire secondary structure upon energy minimization with PyRosetta or YASARA (http://www.yasara.org/minimizationserver.htm).

Thomas



On 9 March 2011 14:59, Claudia Scotti <claudiascotti@hotmail.com> wrote:
Dear All,

Please, I cannot model a beta strand (predicted as such by PSI PRED) in a protein model, even adding further restraints. I think this
depends on the fact that this region is not structured in the templates.

Please, any suggestions (see .py below)?

Many thanks.

Claudia

-------

# Homology modeling with multiple templates
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

class MyModel(automodel):
   def special_restraints(self, aln):
       rsr = self.restraints
       at = self.atoms
#       unpick('1:', '73:')
#       condense('1:', '73:')
#       Add some restraints from a file:
#       rsr.append(file='my_rsrs1.rsr')

#       Residues 49 through 55 should be an alpha helix:
        rsr.add(secondary_structure.alpha(self.residue_range('39:', '45:')))
#       Two beta-strands:
#       rsr.add(secondary_structure.strand(self.residue_range('1:', '5:')))
#       rsr.add(secondary_structure.strand(self.residue_range('19:', '26:')))
#       rsr.add(secondary_structure.strand(self.residue_range('33:', '35:')))
#       rsr.add(secondary_structure.strand(self.residue_range('55:', '58:')))
       rsr.add(secondary_structure.strand(self.residue_range('68:', '72:')))
#       An anti-parallel sheet composed of the two strands:
#       rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'],
#                                         sheet_h_bonds=-5))
#       Use the following instead for a *parallel* sheet:
#       rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'],
#                                         sheet_h_bonds=5))
#       Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1)
#       Use a harmonic potential and X-Y distance group.
#       rsr.add(forms.gaussian(group=physical.xy_distance,
#                              feature=features.distance(at['CA:35'],
#                                                        at['CA:40']),
#                              mean=10.0, stdev=0.1))


a = MyModel(env,
             alnfile  = 'Alignment2.ali', # alignment filename
             knowns   = ('pco','Tas','gen','Rap'),     # codes of the templates
             sequence = 'sALK1')               # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model  = 10                 # index of the last model
                                   # (determines how many models to calculate)
a.make()                            # do the actual homology modeling


--
Claudia Scotti, MD PhD
Department of Experimental Medicine
University of Pavia
Via Ferrata, 1
27100 Pavia
Italy
Tel. 0382 986335
Facs 0382 986893


Claudia Scotti
Dipartimento di Medicina Sperimentale
Sezione di Patologia Generale
Universita' di Pavia
Via Ferrata, 1
27100 Pavia
Italia
Tel. 0039 0382 986335/8/1
Facs 0039 0382 303673


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--

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang@bioacademy.gr

          tevang3@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/