[modeller_usage] disulphide

["Thijs Beuming" <>]

Hi,

I have some problems making a disulphide bridge in MODELLER. Any help  
would be greatly appreciated.

Thanks,

Thijs Beuming

My script:

# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

# 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 176 and 185:
        self.patch(residue_type='DISU', residues=(self.residues['176'],
                                                  self.residues 
['185']))

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 = '~/NTProject2005/NEW_TCA/MODELLER'

a = mymodel(env,
            alnfile  = '~/NTProject2005/NEW_TCA/MODELLER/ 
molpharm.pir',     # alignment filename
            knowns   = '2A65-clean',              # codes of the  
templates
            sequence = 'hNET')              # 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 the actual homology modeling


The error:

 Traceback (most recent call last):
  File "model_hNET_xray2.py", line 26, in ?
    a.make()                            # do the actual homology  
modeling
  File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ 
automodel/automodel.py", line 100, in make
    self.homcsr(exit_stage)
  File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ 
automodel/automodel.py", line 334, in homcsr
    self.generate_method(self, aln)
  File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ 
automodel/generate.py", line 24, in transfer_xyz
    mdl.create_topology(aln)
  File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ 
automodel/automodel.py", line 483, in create_topology
    self.special_patches(aln)
  File "model_hNET_xray2.py", line 10, in special_patches
    self.patch(residue_type='DISU', residues=(self.residues['176'],
  File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ 
model.py", line 543, in __getitem__
    ret = modutil.handle_seq_indx(self, indx)
  File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/util/ 
modutil.py", line 117, in handle_seq_indx
    raise TypeError
TypeError