On Thursday 16 July 2009 10:15:51 Jerry McCully wrote: > > Dear All: > > Next week we are going to try some seleno-Met labeled crystals. > > We checked the literature to try to find out the peak wavelength that > has been used for SAD or MAD data collection. But they are slightly different > ( may be 50 ev) in different papers. > > I guess this is due to the discrepancy between the fluorescence scanning > and the theoretical vaules of f' and f''. > > When we collect the data, which wavelength should we use? Should we > trust the scanning results?
Yes. You should definitely trust the scanning results over any literature value. Let's leave aside for the moment that people may deliberately choose to collect data at 50-100 eV above the peak, and consider only the question of how accurately we can determine what beamline setting corresponds to where the peak is. A fluorescence scan tells you that the fluorescence peak was observed when the monochromator motor readout was N steps (where each step is typically less than 0.001 degree). This is reproducible over the short term, as you should be able to confirm by running the scan again. The nominal energy readout comes from converting the steps to degrees, and then converting the Bragg angle in degrees to an acceptance energy in eV. But these conversion assume a known setting at 0 motor steps, and if this zero point is off by even 0.001 degree that shifts the nominal energy readout near the Se edge by roughly 5 eV as I recall (depends on the monochromator crystal being used). The calibration of the beamline optics is always going to be imperfect, and is subject to minor drift over the course of time. You can ask your friendly neighborhood beamline support people to explain what factors are the most likely to affect calibration of their particular beamline. The usual culprits include heat load on the monochromator or upstream mirrors, and tunable steering of the stored particles in the ring. Not that you can do much about any of this, other than to scan again before collecting your next data set :-) -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
