Hi Nat,

I attached the file and emailed, but it bounced back, saying waiting for approval. Can you please allow me to post it.

Thanks
Suba

On Mon, Feb 6, 2012 at 5:47 PM, Nathaniel Echols <nechols@lbl.gov> wrote:
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.

I'm finding this a little difficult to visualize - do you think you
could make a picture of it in Coot or PyMOL and post that to the list?
 (The server may complain about the message size if it's over 40KB,
but the list administrator [me] can approve it for posting anyway.)

thanks,
Nat
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