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
>>
>>
>>
>>
>>
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