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

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. F. ch. 11.4, p. 232   | 1 | 2 |

Section 11.4.6.1. Refinement of crystal and detector parameters

Z. Otwinowskia* and W. Minorb

a UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA, and bDepartment of Molecular Physiology and Biological Physics, University of Virginia, 1300 Jefferson Park Avenue, Charlottesville, VA 22908, USA
Correspondence e-mail:  zbyszek@mix.swmed.edu

11.4.6.1. Refinement of crystal and detector parameters

| top | pdf |

The precision of the integration step depends on precise knowledge of the peak position. The autoindexing step provides only the approximate orientation of the crystal, and the result of that step is imprecise if the initial values of the detector parameters are poorly known. A nonlinear least-squares refinement process is used to improve the prediction (EEC Cooperative Workshop on Position-Sensitive Detector Software, 1986[link]). Depending on the particulars of the experiment, the same parameters (e.g. crystal-to-detector distance) are more precisely known a priori, or are better estimated from the diffraction data. DENZO allows for the choice of fixing or refining each of the parameters separately. This flexibility is important to characterize a detector, but when detector parameters are already known, the fit all option and detector-specific default values are quite reliable.

DENZO can refine the position and orientation of the detector (six parameters). It can also refine internal parameters of the detector including:

  • (1) curvature radius and rotation of active surface – film rotation, for cylindrical detectors;

  • (2) x to y scale and x to y skew;

  • (3) radial/angular distortion for spiral scanners; and

  • (4) polynomial distortion, separate for each module of multimodule CCD detectors (Naday et al., 1998[link]).

Detector- and crystal-parameter refinement in DENZO is achieved by minimizing the sum of the three functions of the type in equation (11.4.5.1[link]). The contribution resulting from the measurement of position p of the reflection is [\chi_{p}^{2} = {\textstyle\sum\limits_{\rm hkl}} (p_{\rm pred} - p_{\rm cent})^{2}/\sigma_{p}^{2}. \eqno(11.4.6.7)] The measurement of position q contributes a similar term.

References

First citation EEC Cooperative Workshop on Position-Sensitive Detector Software (1986). Phase I and II, LURE, Paris, 16 May–7 June; Phase III, LURE, Paris, 12–19 November.Google Scholar
 First citation Naday, I., Ross, S., Westbrook, E. M. & Zentai, G. (1998). Charge-coupled device/fiber optic taper array X-ray detector for protein crystallography. Opt. Eng. 37, 1235–1244.Google Scholar








































to end of page
to top of page