Diffraction pattern difference intensity maps

Fig. 18. Difference intensity map between diffraction patterns from afully active and a relaxed fish muscle (Mok et aL, 2005). Generally, dark colors show intensity drops and green, yellow, and red show intensity increases. Generally, the myosin layer lines have dropped in intensity (black arrows), and many of the actin layer lines have increased in intensity (white arrows), especially layer line A2. However, the outer part of A1 has dropped in intensity (double-headed black arrow). There are also clearly some shifts in axial spacing of the peaks these are especially visible along the meridian.

In Direct methods, the intensities are extracted from an indexed powder diffraction pattern by profile fitting procedures such as the Le Bail method and Pawley method. Then the integrated intensities obtained are corrected for Torentz polarization and normalized. These corrected intensity values are then subjected to routine Direct-method procedures. The structural model obtained is completed using difference Fourier maps. This method works successfully when a sufficient number of intensities could be extracted from the powder diffraction pattern. 

FIGURE 9.7 Two molecules of tRNA in (a) are related by a twofold symmetry axis along z in the crystal. A point x, y, z, which could be the site of a heavy atom in one molecule, has an identical corresponding site in the dyad-related molecule at — x, —y, z The vector that connects the two sites will be (x, y, z) — (—x, —y, z) = 2x, 2y, 0. This vector, a Harker vector, must appear on the ro = 0 section of the corresponding Patterson map computed from the intensities of the diffraction pattern. In (b) the heavy atom site on the protein molecule at x, y, z appears on the 2i screw axis (along z) related asymmetric unit at —x, —y, Z—. But —, the unit translation, is the same as +, so the difference vector is 2x, 2y,. This Harker vector would appear on the plane of the Patterson map containing points for which w =. ... 

Crucial to the success of ab initio structure determinations is the collection of 3-D diffraction data. The conventional TEM sample holders can handle limited rotation (up to 35° e.g., in some HREM), which leaves a wedge-shaped gap in reciprocal space. Special holders used for tomography with a large rotation range can be used to address this problem. The diffraction patterns recorded at different rotations are merged to produce the 3-D data set. Special care must be taken to normalize the diffraction intensities because of the 3-D shape of the crystal and possible dynamic diffraction effects. In the absence of 3-D diffraction data set, diffraction patterns can be recorded along zone-axis orientations and reconstructed to obtain the projection maps. These maps then... 

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