I would be a bit more concerned with the apparent lack of fit of the model to
the map. It looks as if there is unoccupied side chain density, and possibly
side chains that don't occupy density. It is hard to tell from a snapshot, but
if this is the case, make sure everything is in register first, then re-refine,
having reset the temperature factors to something sensible, and then when you
converge on something that fits and makes sense, re-assess the map. Lots of
green density sitting on your model might indicate problems with scaling the
data or with the temperature factor refinement.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax: +1-831-4593139 (fax)
On Jan 25, 2012, at 8:04 PM, Dialing Pretty wrote:
> Dear All,
>
> Will you please take a loot on the coot sscreenshot and give me some
> suggestions on how to further optimize in order to have the green blobs
> disappear by Coot?
>
> Cheers,
>
> Dialing
