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Hi Ivan, https://csgid.org/csgid/metal_sites/ suggest that Mg++ is the correct metal. Ca++ is not acceptable. I am going to validate it by calculating anomalous peak for Ca++ too. Thank you Rajesh On Wed, Mar 7, 2018 at 1:06 PM, Ivan Shabalin < [log in to unmask]> wrote: > 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: > > https://csgid.org/csgid/metal_sites/ > > > 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: > > http://skuld.bmsc.washington.edu/scatter/AS_periodic.html > > Ivan > > > > With best regards, > Ivan Shabalin, Ph.D. > Research Scientist, > Department of Molecular Physiology and Biological Physics, > University of Virginia, > 1340 Jefferson Park Avenue > <https://maps.google.com/?q=1340+Jefferson+Park+Avenue&entry=gmail&source=g>, > 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. >> >> -Rajesh >> >> >> >> >> > ---- >