[modeller_usage] loop modeling limits

[lorix <>]

Dear users,
I would like to build part of a protein which is missing from the PDB file.
It is a very long loop (72 residues) and I am not sure if the task is 
beyond Modeller skills.
I have information about secondary structure elements of this protein 
part (three helices and a strand) thus
I tried to use them as restrains in the program but what I got after 
increasing the  automodel.max_molpdf (because it did not produce any 
results with the default limit) was just a long flat and linear loop 
without any apparent secondary structure.
Might be I did not check enough into the available literature about the 
program and there are ways to model such a loop or
it is just not possible. Can someone, please, help me with a suggestion?

that's the input file:

#  Homology modelling by the automodel class with special restrains for 
secondary structure

from modeller.automodel import *         # Load the automodel class

# Redefine the special_restraints routine to include the secondary
# structure restraints (this routine is empty by default):
class mymodel(automodel):
   def special_restraints(self, aln):
       rsr = self.restraints
       # Three alpha-helix:
       rsr.make(aln, restraint_type='ALPHA', residue_ids=('143', '148'),
                spline_on_site=False)
       rsr.make(aln, restraint_type='ALPHA', residue_ids=('195', '200'),
                spline_on_site=False)
       rsr.make(aln, restraint_type='ALPHA', residue_ids=('204', '206'),
                spline_on_site=False)
       # One strand:
       rsr.make(aln, restraint_type='STRAND', residue_ids=('171', '174'),
                spline_on_site=False)

log.verbose()
env = environ()

# directories for input atom files
env.io.atom_files_directory = './'

a = mymodel(env,
           alnfile='protein_full.ali',        # alignment filename
           knowns='PDB_refined',            # codes of the templates
       sequence='protein_full')            # code of the target

a.starting_model= 1                 # index of the first model
a.ending_model  = 3                 # index of the last model
                                   # (determines how many models to 
calculate)


a.max_molpdf = 500000            # define the max of molec probability 
density function

a.md_level = refine.fast                   # type of refinement of model


a.make()


thanks
loris...