[modeller_usage] set alpha-helix and SS bond

[Aline <>]

Hi list,

Im trying to model a 5 chains protein, wich 3 of them are long alpha-helix.
Well, I would like to set some residues as part of these helixes, and
a SS bridge.
When I try to tell modeller 9v1 to do that (with the enclose script),
I keep receiving  the following error:
----------------------------------------------------------------------------
C:\teste2>mod9v1 model_ss_alpha.py
'import site' failed; use -v for traceback
Traceback (most recent call last):
 File "model_ss_alpha.py", line 31, in ?
   a.make()
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel
.py", line 108, in make
   self.homcsr(exit_stage)
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel
.py", line 419, in homcsr
   self.make_initial_model(aln)
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel
.py", line 433, in make_initial_model
   self.generate_method(self, aln)
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\generate.
py", line 25, in transfer_xyz
   mdl.create_topology(aln)
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel
.py", line 605, in create_topology
   self.special_patches(aln)
 File "model_ss_alpha.py", line 18, in special_patches
   self.patch(residue_type='DISU', residues=(self.residues['1070'],
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\coordinates.py", li
ne 165, in __getitem__
   (self.offset, self.length, self.suffix))
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\util\modutil.py", l
ine 76, in handle_seq_indx
   int_indx = lookup_func(*args)
 File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\coordinates.py", li
ne 50, in _indxres
   raise KeyError, ("No such residue: %s" % indx)
KeyError: 'No such residue: 1070'
--------------------------------------------------------------------------
What might be wrong?

Thanks,

Aline



-------------------------------------------------------------------
This is the script:


from modeller import *              # Load standard Modeller classes
from modeller.automodel import *

# 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
       # An alpha-helix:
       rsr.make(aln, restraint_type='ALPHA', residue_ids=
('1118:', '1131:'),
                spline_on_site=False)
# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class mymodel(automodel):
   def special_patches(self, aln):
       # A disulfide between residues 8 and 45:
       self.patch(residue_type='DISU', residues=(self.residues['1070'],
                                                 self.residues['1122']))

# This is as usual:
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directory = './:../atom_files'
env.io.hetatm = env.io.water = True
a = mymodel(env, alnfile='a6b1lam.ali',
             knowns=('a6b1lam_model_0.3'), sequence='a6b1_lam')
a.starting_model = 1
a.ending_model = 1
a.make()