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!
# 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
Lixia Jin wrote: > 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!
Your script looks fine to me. As for why you're not seeing the disulfide bond, this could have two explanations:
1. Modeller does not add any connectivity information to the generated PDB file. So your PDB viewer will not "know" to draw a disulfide bond. Some viewers will just try to guess if such a bond exists by looking at the distances between residues.
2. It may be that your structure is very strained, or the template information strongly disagrees with the disulfide you've added, so that the disulfide restraints cannot be satisfied. In that case, you should see the violations of these restraints in your log file.
Ben Webb, Modeller Caretaker