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Re: [modeller_usage] R: question for a (putative?) disulfide bridge

Anna Marabotti wrote:
> thank you for your message, and sorry to bother you again. I tried to
> use model.patch() to add the disulfide
> bridge to my model, but I have a supplementary problem. In fact, my
> protein is a homodimer and the disulfide
> bridge should link two Cys residues in the two different subunits. I
> tried to indicate "A" and "B" in the
> script in this way:
> # Create the disulfide bond:
> def patches(mdl):
>     mdl.patch(residue_type='DISU', residues=(mdl.residues['55:A.'],
>                                              mdl.residues['180:B']))
> but it doesn't work.

What do you mean by "it doesn't work"? You get an error message (what is
it?) or everything runs but the disulfide isn't created? In the latter
case, I'd need to see the full script. In the former case, you probably
have the wrong residue numbers and/or chains for your two Cys residues.
The first residue should probably be '55:A' rather than '55:A.' but one
way to check the numbers is to run modeling first without the patch, and
look at the numbers in the generated model.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage