Iterative peaklist optimization

Sheldrick, G. M.; Hauptman, H. A.; Weeks, C. M.; Miller, R.; Usón, I.

doi:10.1107/97809553602060000689

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

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International Tables for Crystallography (2006). Vol. F. ch. 16.1, p. 336 | 1 | 2 |

Section 16.1.5.2. Iterative peaklist optimization

G. M. Sheldrick,^c H. A. Hauptman,^b C. M. Weeks,^b ^* R. Miller^b and I. Usón^a

^a Institut für Anorganisch Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany,^bHauptman–Woodward Medical Research Institute, Inc., 73 High Street, Buffalo, NY 14203-1196, USA, and ^cLehrstuhl für Strukturchemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
Correspondence e-mail: weeks@orion.hwi.buffalo.edu

16.1.5.2. Iterative peaklist optimization

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An alternative approach to peak picking is to select approximately $[N_{u}]$ peaks as potential atoms and then eliminate some of them, one by one, while maximizing a suitable figure of merit such as $[P = \textstyle\sum\limits_{\bf H} |E_{c}^{2}| (|E_{o}^{2}| - 1). \eqno(16.1.5.1)]$ The top $[N_{u}]$ peaks are used as potential atoms to compute $[|E_{c}|]$ . The atom that leaves the highest value of P is then eliminated. Typically, this procedure, which has been termed iterative peaklist optimization (Sheldrick & Gould, 1995), is repeated until only $[2N_{u}/3]$ atoms remain. Use of equation (16.1.5.1) may be regarded as a reciprocal-space method of maximizing the fit to the origin-removed sharpened Patterson function, and it is used for this purpose in molecular replacement (Beurskens, 1981). Subject to various approximations, maximum-likelihood considerations also indicate that it is an appropriate function to maximize (Bricogne, 1998). Iterative peaklist optimization provides a higher percentage of solutions than simple peak picking, but it suffers from the disadvantage of requiring much more CPU time.

References

Beurskens, P. T. (1981). A statistical interpretation of rotation and translation functions in reciprocal space. Acta Cryst. A37, 426–430.Google Scholar

Bricogne, G. (1998). Bayesian statistical viewpoint on structure determination: basic concepts and examples. Methods Enzymol. 276, 361–423.Google Scholar

Sheldrick, G. M. & Gould, R. O. (1995). Structure solution by iterative peaklist optimization and tangent expansion in space group P1. Acta Cryst. B51, 423–431.Google Scholar

International Tables for Crystallography (2006). Vol. F. ch. 16.1, p. 336