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
Lixia Jin wrote: > 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'
Just as the error says, you have no 199:G residue in your model. Note that the labeling of model residues is not the same as your template residues. Do an ordinary automodel run first and look at the generated .ini or .pdb files if you are unsure.
Ben Webb, Modeller Caretaker
participants (2)
-
Lixia Jin -
Modeller Caretaker