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. 18.5, pp. 404-405
Section 18.5.2.3. Statistical descriptors and goodness of fit^{a}Chemistry Department, UMIST, Manchester M60 1QD, England |
In recent years, there have been developments and changes in statistical nomenclature and usage. Many aspects are summarised in the reports of the IUCr Subcommittee on Statistical Descriptors in Crystallography (Schwarzenbach et al., 1989, 1995). In the second report, inter alia, the Subcommittee emphasizes the terms uncertainty and standard uncertainty (s.u.). The latter is a replacement for the older term estimated standard deviation (e.s.d.). The Subcommittee classify uncertainty components in two categories, based on their method of evaluation: type A, estimated by the statistical analysis of a series of observations, and type B, estimated otherwise. As an example of the latter, a type B component could allow for doubts concerning the estimated shape and dimensions of the diffracting crystal and the subsequent corrections made for absorption.
The square root S of the expression S^{2}, (18.5.2.12) above, is called the goodness of fit when the weights are the reciprocals of the absolute variances of the observations.
One recommendation in the second report does call for comment here. While agreeing that formulae like (18.5.2.13) lead to conservative estimates of parameter variances, the report suggests that this practice is based on the questionable assumption that the variances of the observations by which the weights are assigned are relatively correct but uniformly underestimated. When the goodness of fit , then either the weights or the model or both are suspect.
Comment is needed. The account in Section 18.5.2.2 describes two distinct ways of estimating parameter variances, covering two ranges of error. The kind of weights envisaged in the reports (based on variances of type A and/or of type B) are of a class described for method (1). They are not the weights to be used in method (2) (though they may be a component in such weights). Method (2) implicitly assumes from the outset that there are experimental errors, some covered and others not covered by method (1), and that there are imperfections in the calculated model (as is obviously true for proteins). Method (2) avoids exploring the relative proportions and details of these error sources and aims to provide a realistic estimate of parameter uncertainties which can be used in external comparisons. It can be formally objected that method (2) does not conform to the criteria of random-variable theory, since clearly the Δ's are partially correlated through the remaining model errors and some systematic experimental errors. But it is a useful procedure. Method (1) on its own would present an optimistic view of the reliability of the overall investigation, the degree of optimism being indicated by the inverse of the goodness of fit (18.5.2.12). In method (2), if the weights are on an arbitrary scale, then can have an arbitrary value.
For an advanced-level treatment of many aspects of the refinement of structural parameters, see Part 8 of International Tables for Crystallography, Volume C (2004). The detection and treatment of systematic error are discussed in Chapter 8.5 therein.
References
International Tables for Crystallography (2004). Vol. C. Mathematical, physical and chemical tables, edited by E. Prince. Dordrecht: Kluwer Academic Publishers.Google ScholarSchwarzenbach, D., Abrahams, S. C., Flack, H. D., Gonschorek, W., Hahn, Th., Huml, K., Marsh, R. E., Prince, E., Robertson, B. E., Rollett, J. S. & Wilson, A. J. C. (1989). Statistical descriptors in crystallography: Report of the IUCr subcommittee on statistical descriptors. Acta Cryst. A45, 63–75.Google Scholar
Schwarzenbach, D., Abrahams, S. C., Flack, H. D., Prince, E. & Wilson, A. J. C. (1995). Statistical descriptors in crystallography. II. Report of a working group on expression of uncertainty in measurement. Acta Cryst. A51, 565–569.Google Scholar