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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
