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 > > > >
