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
>
>
>
>
|