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Hi Ethan:
Gosh, it's almost as if f' and f" are not independent quantities but
simply Kramers-Kronig transforms of the same physical phenomenon.
So even if I have the correct fcalc (based on the corrected Mn scattering
factor at the f' peak), or, calculate just an Fobs map, the density at
the Mn sites will all be anomalously weak, which in turn means if I don't
want a funny-looking map, I ought to use the remote data, not the
inflection.
Thanks. It should have been obvious. I even teach this stuff in my sleep
(which I guess is the ultimate root of the problem).
All the best,
Bill
On Fri, 28 Jul 2006, Ethan Merritt wrote:
On Friday 28 July 2006 04:36 pm, William Scott wrote:
I'm refining a previously solved RNA structure in which we have
soaked 10 mM Mg++ and collected data near the absorption edge.
The most striking difference is in the 2Fo - Fc maps.
http://www.chemistry.ucsc.edu/~wgscott/temp/weirdmaps.pdf
Maybe this has been pointed out already, but...
The real component of the anomalous scattering (f') at the
inflection point is negative. If you have a well-tuned beamline
and good mosaicity, it could be a large as -10e. So in the
inflection point data, the real component of Mn scattering is
reduced compared to data collected at other energies.
Let's oversimplify this by saying "Fobs is smaller".
But unless you have provided refmac with a new set of scattering
factors, it is still using the Mn f' term corresponding to the
X-ray scattering at the Cu K-alpha emission energy (-1e).
Let's oversimplify this by saying "Fcalc is still big".
So, when you calculate the 2Fobs-Fcalc map you are damping the
size of the Mn peak, possibly by as much as 18 electrons.
Anyway, the simple answer to my question is to use the remote data
for refinement, but had we not collected multiple wavelength data
sets on this metal soak, is there a way that I could more reliably
model the Mn++ scattering at the inflection point?
Give refmac a proper set of scattering factors for the wavelength
your data was collected at. This is controlled by the input file
name ATOMSF. The default file is in ${CLIB}/data/atomsf.lib
But the contribution of a metal atom at the inflection point of
its absorption edge really is smaller, so even with the correct
scattering factors in place you should still expect a lower peak
in the maps made from this X-ray energy.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle WA
