On 30/11/12 10:05, Almudena Ponce Salvatierra wrote:
>
>
> I would like to know if it is possible to use either the "real space
> refine zone" or the "regularize zone" tools just between two atoms in
> a cofactor molecule.
Do you mean by that that you don't want the other atoms to move?
Yes, you can do that, I'm not sure that I'd advise it.
> It works perfectly between two atoms when I use it on the protein, but
> it doesn't when I try to model the cofactor.
Somewhat unclear what the problem is. Do you mean that in the protein
you can refine a bond when clicking on two atoms in different residues,
however, the co-factor, which is also comprise of more than one residue
(monomer) this doesn't work?
(Presumably this is not what you mean.)
> Instead of picking just the two atoms I'm interested in, it picks the
> whole cofactor molecule.
OK, so to fix the other atoms, use the anchor tool to fix the atoms that
you don't want to move.
>
> I'm experiencing problems to validate this structure because most of
> the outliers come from the cofactor and I'm not able to fix them.
>
What does "validate" mean here? What is the metric for the outliers?
(I rather suspect an issue with the restraints, not the refinement)
Paul.
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