International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 11.2, pp. 212-213   | 1 | 2 |

Section 11.2.4. The measurement box

A. G. W. Lesliea*

aMRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
Correspondence e-mail: andrew@mrc-lmb.cam.ac.uk

11.2.4. The measurement box

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X-ray scattering from air, the sample holder and the specimen itself gives rise to a general background in the images which has to be subtracted in order to obtain the Bragg intensities. Ideally, the background should be measured for the same pixels used to record the Bragg diffraction spot, but this is not usually practical and the background is determined using pixels immediately adjacent to the spot. In practice, the pixels to be used for the determination of the background (background pixels) and those to be used for evaluating the intensity (peak pixels) are defined using a `measurement box'. This is a rectangular box of pixels centred on the predicted spot position. Each pixel within the box is classified as being a background or a peak pixel (or neither). This mask can either be defined by the user, or the classification can be made automatically by the program. An example of a possible measurement-box definition is given in Fig. 11.2.4.1[link]. The background parameters NRX, NRY and NC can be optimized automatically by maximizing the ratio of the intensity divided by its standard deviation, in a manner analogous to that described by Lehmann & Larsen (1974[link]). It is generally assumed that the background can be adequately modelled as a plane, and the plane constants are determined using the background pixels. This allows the background to be estimated for the peak pixels, so that the background-corrected intensity can be calculated.

[Figure 11.2.4.1]

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The measurement-box definition used in MOSFLM. The measurement box has overall dimensions of NX by NY pixels (both odd integers). The separation between peak and background pixels is defined by the widths of the background rims (NRX and NRY) and the corner cutoff (NC). The size of the peak region is optimized separately for each of the standard profiles.

References

Lehmann, M. S. & Larsen, F. K. (1974). A method for location of the peaks in step-scan-measured Bragg reflexions. Acta Cryst. A30, 580–584.








































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