On Thu, 28 Oct 2010 16:56:42 +0200
Dirk Kostrewa <kostr...@genzentrum.lmu.de> wrote:
>
> In the Babinet bulk solvent correction, no bulk solvent phases are
> used, it is entirely based on amplitudes and strictly only valid if
> the phases of the bulk solvent are opposite to the ones of the
> protein. And as Sasha Urzhumtsev pointed out, this assumption is only
> valid at very low resolution.
>
> The mask bulk solvent correction is a vector sum including the phases
> of the bulk solvent mask, which makes a difference at medium
> resolution (up to ~4.5 A, or so).
>
> As far as I can see, your formulas given below do not distinguish
> between amplitude (modulus) and vector bulk solvent corrections.
>
Sorry - I didn't make that clear. The formulas all use complex
structure factors, as in the paper.
> Personally, I really don't see any physical sense in using both
> corrections together, except for compensating any potential scaling
> problems at low resolution.
>
We're not using "both corrections together" - the Babinet *method* is
used to add in the bulk solvent contribution computed using the flat
mask *model* (or the polynomial/Gaussian model in the paper). The
protein structure factors (Fc) are not used in the bulk solvent
correction - nor, in my opinion, should they be (as I attempted to
point out in my previous email).
Regards,
Tim
--
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Tim Fenn
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Stanford University, School of Medicine
James H. Clark Center
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