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You just calculate a anom map - it doesnt need you to dselect Ca or Mg or anything else.. Judge the peak heights by the signal you get over any S sites in the model. The relative signal you expect depends on your wavelength of course. Eleanor On 7 March 2018 at 19:09, Rajesh Kumar <[log in to unmask]> wrote: > 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] > edu> 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 >>> >>> >>> >>> >>> >> ---- >> > >