Dear Lijun Liu,
You can use the CCP4 prog sftools to determine if there are
just a few strong reflections.
Adam
On Tue, 20 Jul 2010, Lijun Liu wrote:
> Hi all,
>
> I solved a structure and the refinement is close to complete.
> However, some residual density puzzles me.
>
> The SG is P212121, and the c is 84.8 Å. Along c, in several small but
> not all regions, there are some layered, alternately appeared positive
> and negative residual density pieces (c is the norm of these plane-
> like pieces; 3-sigma contour for pos and neg difference densities).
> The distance between the neighboring positive pieces is measured to be
> ~2.1 Å, corresponding to ~1/40 *c. In one of such region, there is an
> indole ring of Trp that is approximately parallel to the plane-like
> residual density pieces (attached figure). In two other regions,
> there are Leu or else but not ring structure.
>
> The data is complete to 1.9 Å. Reflection check did not show any
> special imcompleteness (ice ring loss, wedge loss, other resolution
> bin loss, etc). It looks like to me that there is a systematic loss
> of information which made it is specially sensitive to ~2.1 Å
> reflections (especially those along c*). It does not look like to me
> to be radiation damage. Crystal was needle and showed somehow
> polarized (but never serious) diffraction pattern along c*.
>
> Attached is a piece of map with the above-mentioned Trp included. I
> would like to know if some one also met something like this before.
> Thanks for any comments.
>
> Lijun Liu
> Cardiovascular Research Institute
> University of California, San Francisco
> 1700 4th Street, Box 2532
> San Francisco, CA 94158
> Phone: (415)514-2836
>
>
>
>
