Hi Sacha is absolutely right here. This was made plain to me during a plenary session at the recent BCA meeting in Warwick, given by a powder (not protein) crystallographer - who was using histogram matching density modification, with negative densities; an expert in density modification in protein crystallography tells me that "using a map with no truncation (and hence no negative densities) always gives rubbish results in my hands".
On 9 Jul 2010, at 06:37, Alexandre Urzhumtsev wrote: > 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 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
