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
