When I use: self.patch(residue_type='DISU', residues=(self.residues['199'], self.residues['205'])) it works. When I use: self.patch(residue_type='DISU', residues=(self.residues ['199:G'], self.residues ['205:G'])) it gives me error information: KeyError: 'No such residue: 199:G'
What might be wrong? Thanks!
------ 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