Hi Nat,<div><br></div><div>I have attached a picture of that area with this. The rotamer I am refering to is ASP 26.</div><div><br></div><div>Thanks</div><div>Subhani<br><br><div class="gmail_quote">On Mon, Feb 6, 2012 at 5:47 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5">On Mon, Feb 6, 2012 at 3:42 PM, Subhani Bandara <<a href="mailto:ramssb17@gmail.com">ramssb17@gmail.com</a>> wrote:<br>
> I have a protein cocrystallized with a metal chelator complex. The side<br>
> chain of a Asp residue has density around one of the chelators(oxygen atom).<br>
> The positive density for the rotamer of Asp is seen too close to chelator<br>
> oxygen(~1.17 A) and therefore rotamer is moving into a negative density.<br>
><br>
> �When I correct the rotamer and refine, it again come back to the same<br>
> place, due to repulsive forces I guess. then I moved ligand away and refined<br>
> with�corrected rotamer, but after refinement ligand is again back at the<br>
> same position, as well as the rotamer. How can I fix this? Does this<br>
> indicate that the ligand may �not be there although I see some density for<br>
> it(full density is seen ~0.79 sigma and partial density ~1.00 sigma). Also<br>
> is this happening due to the memory of ligand position in phenix.<br>
<br>
</div></div>I'm finding this a little difficult to visualize - do you think you<br>
could make a picture of it in Coot or PyMOL and post that to the list?<br>
�(The server may complain about the message size if it's over 40KB,<br>
but the list administrator [me] can approve it for posting anyway.)<br>
<br>
thanks,<br>
<div class="HOEnZb"><div class="h5">Nat<br>
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