On Mon, Feb 6, 2012 at 3:42 PM, Subhani Bandara <
ramssb17@gmail.com> wrote:
> I have a protein cocrystallized with a metal chelator complex. The side
> chain of a Asp residue has density around one of the chelators(oxygen atom).
> The positive density for the rotamer of Asp is seen too close to chelator
> oxygen(~1.17 A) and therefore rotamer is moving into a negative density.
>
> When I correct the rotamer and refine, it again come back to the same
> place, due to repulsive forces I guess. then I moved ligand away and refined
> with corrected rotamer, but after refinement ligand is again back at the
> same position, as well as the rotamer. How can I fix this? Does this
> indicate that the ligand may not be there although I see some density for
> it(full density is seen ~0.79 sigma and partial density ~1.00 sigma). Also
> is this happening due to the memory of ligand position in phenix.