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)