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:
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: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
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