Hi, Rajesh,

It does look like Ca to me. It has around 2.4 A distances to waters and quite many electrons (18), which correspond to rather wide and high density peak in the middle.

Mg has distances at 2.07, and 10 electrons (should be a smaller peak).

Na has 2.41 distances to waters, 10 electrons (should be a smaller peak).

After you place a metal and refine it, try using CheckMyMetal to validate it:


It takes into account preferable coordination geometries, coordination bond distances, and compares ADPs to average ADP for the surrounding atoms.

If the dataset is very good, and the wavelength of X-ray is rather long, you might even get anomalous signal for Ca:



With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908

On 03/06/2018 05:19 PM, Rajesh Kumar wrote:
Dear All,

Have you had experience with this kind of density? I am wandering what this could be?

Thank you very much for the help.



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