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 -- http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage