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
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