[modeller_usage] define residues

["Lixia Jin" <>]

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