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