[modeller_usage] disulfide

["Lixia Jin" <>]

Hi,

First try MODELLER.

It worked good. Then I added DISU as I learned from the manual by redefining the special_patches().  (Script as below) The new model is the same as the old one. I don't see disulfide bond between the two cysteins. 

Can any one explain it a bit? Thank you!

 

Lixia

------------------

 

# 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 199-205
   self.patch(residue_type='DISU', residues=(self.residues['199'],
               self.residues['205']))

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 = './:..'

a = mymodel(env,
              alnfile  = 'align2.ali',     # alignment filename
              knowns   = 'e791',              # codes of the templates
              sequence = 'spnG')              # 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