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Uhh. No. You will only get "imaginary" electron density if your structure factors violate Friedel's law. I am not aware of map calculation codes that do this (on purpose). BTW, "imaginary electrons" are really just "slow" electrons that don't respond to the x-rays as fast as the "average" electron in the unit cell. They can also be "faster" than average. Because of this, if you have a unit cell full of nothing but selenium atoms, you will get all Bijvoet differences equal to zero. Even at the selenium edge! -James Holton MAD Scientist Hailiang Zhang wrote: > Dear Sacha: > > Yes, I think Fourier synthesis at a finite resolution range will generate > some negative, or more generally imaginary values in real space (hope I am > right again:). For the imaginary values, I think the map should take the > amplitude of it (maybe I am wrong). Do they normally make the density > negative when the real-space density "phase angle" is between 90-270 > degree, and positive other wise, or something else? > > Thanks a lot! > > Best Regards, Hailiang > > > >> Dear Hailiang, >> >> >>> This apparently is not the real physics, since the >>> electron density has to be positive everywhere (hope I am right). >>> >> Yes, you are right when you are talking about the electron density. >> >> You are wrong when you are talking about a Fourier synthesis calculated >> always at a finite resolution (it is what you have, is it?), even when the >> term F000 is used as suggested. >> >> Such a synthesis MUST have NEGATIVE values due to Fourier series >> truncation. Allowing such negative values was an important point at the >> beginning of density modification procedures (beginning of 80th) and it >> was >> one of the key moments when developping electron density histograms (see >> for example Lunin, 1988, Acta Cryst A). Moreover, these points even >> contain >> some information and can be used for example to identify the >> macromolecular >> region (since the deepest minima are usually close to the highest maxima). >> >> With best regards, >> >> Sacha >> >> >> >> >>