[modeller_usage] HELP!! Refine part of model

["Matt wagner" <>]

I am refining a segment of my model using the refine part of model script ( 
http://salilab.org/modeller/manual/node28.html).  Everything works fine, but 
it creates so many atom clashes that when I do an energy minimization on the 
structure, that the backbone of my protein snaps.  Is there another way to 
reduce these atom clahses? I also did a test in which I turned on bond 
interactions, by setting env.edat.nonbonded_sel_atoms = 1; but there are 
still too many atom clashes.   Below is a copy of my script:

# Addition of restraints to the default ones

from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

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

class mymodel(automodel):
   def special_restraints(self, aln):
       rsr = self.restraints
#       Add some restraints from a file:
#       rsr.append(file='my_rsrs1.rsr')
#       Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1)
#       Use a harmonic potential and X-Y distance group.
       rsr.add(atom_ids=('NZ:12', 'NZ:23'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 11.0, 0.01))
       rsr.add(atom_ids=('NZ:40', 'NZ:45'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 9.5, 0.01))
       rsr.add(atom_ids=('NZ:88', 'NZ:94'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 10.4, 0.01))
       rsr.add(atom_ids=('NZ:94', 'NZ:96'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 10.4, 0.01))
       rsr.add(atom_ids=('NZ:96', 'NZ:106'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 11.4, 0.01))
       rsr.add(atom_ids=('NZ:106', 'NZ:107'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 6.5, 0.01))
       rsr.add(atom_ids=('NZ:133', 'NZ:140'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 11.4, 0.01))
       rsr.add(atom_ids=('NZ:206', 'NZ:208'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 3.8, 0.01))
       rsr.add(atom_ids=('NZ:226', 'NZ:238'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 34.2, 0.01))
       rsr.add(atom_ids=('NZ:238', 'NZ:239'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 6.9, 0.01))
       rsr.add(atom_ids=('N:1', 'NZ:96'),restraint_parameters=(3, 1, 1, 27, 
2, 2, 0, 11.4, 0.01))
       rsr.add(atom_ids=('NZ:23', 'NZ:59'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 7.5, 0.01))
       rsr.add(atom_ids=('NZ:94', 'NZ:208'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 4.5, 0.01))
       rsr.add(atom_ids=('NZ:96', 'NZ:195'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 10.3, 0.01))
       rsr.add(atom_ids=('NZ:96', 'NZ:208'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 7.2, 0.01))
       rsr.add(atom_ids=('NZ:96', 'NZ:226'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 11.4, 0.01))
       rsr.add(atom_ids=('NZ:118', 'NZ:140'),restraint_parameters=(3, 1, 1, 
27, 2, 2, 0, 11.4, 0.01))
       rsr.make(aln, restraint_type='ALPHA', residue_ids=('24', '39'), 
spline_on_site=False)
       rsr.make(aln, restraint_type='ALPHA', residue_ids=('48', '82'), 
spline_on_site=False)
       rsr.make(aln, restraint_type='ALPHA', residue_ids=('100', '129'), 
spline_on_site=False)
       rsr.make(aln, restraint_type='ALPHA', residue_ids=('134', '164'), 
spline_on_site=False)

   def select_atoms(self):
       self.pick_atoms(selection_segment=('87:', '113:'),
                       selection_search='segment', pick_atoms_set=1,
                       res_types='all', atom_types='all',
                       selection_from='all', selection_status='initialize')


env = environ()
# directories for input atom files
env.io.atom_files_directory = './:../atom_files'
# selected atoms do not feel the neighborhood
env.edat.nonbonded_sel_atoms = 2

a = mymodel(env,
           alnfile  = 'TvLDH-mult.ali',
           knowns   = ('1_86','114_243'),
           sequence = 'TvLDH')              # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model  = 1                 # index of the last model
                                   # (determines how many models to 
calculate)
a.make()                            # do homology modelling