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