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Re: [modeller_usage] Including disulfide bonds

Atila Iamarino wrote:
I'm interested in modeling a protein forcing disulfide bridges but my protein has two chains. How do I set the residue in the .py file? 

# 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['8'],
                                                  self.residues['45']))
That's straightforward - just include a chain ID (see http://salilab.org/modeller/9v1/manual/node153.html). For example, 

    self.patch(residue_type='DISU', residues=(self.residues['8:A'],
                                              self.residues['45:A']))

	Ben Webb, Modeller Caretaker
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