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See also the tutorial worksheet.
3a) Scaling and analysing datasetsf' and f'' for Se varies with wavelength as (output from program crossec):
We have data for 4 wavelengths, labelled as:
But:
Normal Probability plotsSee Lynne Howell and Dave Smith, J.Appl. Cryst. 25 81-86 (1992)3b) Preparing datasets for finding heavy atomsNormalised Structure FactorsMost direct methods procedures make use of normalised structure factors (denoted E) rather than the bare structure factor amplitude F. The value of E for a reflection is defined as F divided by the product of epsilon (a factor dependent on the Laue group symmetry) and the r.m.s. value of the structure amplitudes at its sin(theta)/lambda value. The values of E therefore do not fall off with increasing scattering angle.See C.Giacovazzo et al, Fundamentals of Crystallography, p.321 In CCP4, the program ECALC is used to derive Es from Fs. These can then be used in the direct methods program RANTAN. 3c) Find heavy atomsHeavy atom positionsWhen trying to understand heavy atom positions, remember to consider symmetry equivalent positions. Also, depending on the spacegroup, there may be alternative origins. Finally, there are 2 possible hands for each set of positions.The current example is in spacegroup C2. This is a polar spacegroup, so that the origin is not fixed along the b axis. In addition, there are 4 possible origins in the a-c plane: Norigin Xo Yo Zo 1 0.0000 0.0000 0.0000 2 0.0000 0.0000 0.5000 3 0.5000 0.0000 0.0000 4 0.5000 0.0000 0.5000 Heavy atom sites from different phase sets output from RANTAN may be with respect to different origins. For example, the first 3 sites from phase set 1 are: 0.26 0.06 0.75 0.43 0.24 0.38 0.20 0.45 0.36The opposite hand would also be a solution: -0.26 -0.06 -0.75 -0.43 -0.24 -0.38 -0.20 -0.45 -0.36 We can then change the origin to -0.5,-0.24,-0.5 (origin 4 above, plus a shift along the b axis): 0.24 0.18 0.75 0.07 0.00 0.12 0.30 0.79 0.14 Finally, we find a symmetry mate of site 3 by applying the symmetry operation 1/2-X,1/2+Y,-Z: 0.24 0.18 0.75 0.07 0.00 0.12 0.20 0.29 0.86These are in fact the first 3 sites of phase set 2!! 3d) Heavy atom refinementDescribe Derivatives and RefinementIn MAD, the "derivatives" correspond to different wavelengths of the same derivative (e.g. a 3 wavelength Se-Met MAD experiment would give 3 "derivatives"). When refining heavy atom positions for each "derivative", you are actually refining the same heavy atom coordinates (e.g. Se coordinates) against different data for the different wavelengths.For each heavy atom, you can refine its XYZ coordinates, its occupancy and its B factor. For each "derivative" or wavelength, you can refine the heavy atom parameters against:
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