Dear Bernhard,
further thinking about the Babinet scaling effects, I have to
correct my conclusion in the last sentence:
On 12.01.2015 14:21, Dirk Kostrewa
wrote:
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type="cite">
If, however, the unmodelled part is less well ordered (which is
the more common case), it's contribution will mainly affect the
model's Fcalc at low resolution. If the overall scaling is
dominated by the high resolution terms (which is usually the
case), the unmodelled part will not have an effect on the overall
scale factor of the model's Fcalc, leaving only the Fcalc at low
resolution somewhat too low. Since lowering the model's Fcalc
scale factor at low resolution is the main purpose of the Babinet
solvent correction, this will lead to an _underestimation_ (!) of
the Babinet bulk solvent contribution scale factor (ksol). This,
in principle, should increase, or overestimate, the signal of the
difference densities at low resolution, which might also help with
interpretation of the unmodelled part.
The underestimation of the Babinet bulk solvent scale factor is
equivalent to an overestimation of the contrast between protein and
solvent and should therefore lead to an overestimation of the Fcalc
at low resolution. If scaling is still dominated by the high
resolution terms, this should lead to a decrease, or
underestimation, of the structure factor differences at low
resolution, which would reduce the overall signal of the difference
densities. But still, this will be an overall effect and not
restricted to the location of the unmodelled part.
Best regards,
Dirk.
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [log in to unmask]
WWW: www.genzentrum.lmu.de
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