On Tue, Nov 6, 2012 at 12:06 PM, saleem raza <[email protected]> wrote: > I have to put water molecules in my model but It's difficult to judge that > electron density is for water of something else. How to differentiate???? > > How the electron density look like for metal ions like Ca and Na???
Sodium can't be distinguished from water on the basis of electron density. You can use the bond valence method (e.g. a program like WASP) to identify likely sodium ions, but this requires good data and relatively high resolution. Calcium has nearly twice as many electrons as water, and should be very obvious in the Fo-Fc map (assuming you've built in a water to start with) unless it's only present at half occupancy. Depending on the wavelength you collected at and the quality of the data, you may also be able to see a peak in the anomalous difference map. The chemical environment tends to be more distinctive than sodium too. -Nat
