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

International Tables for Crystallography (2012). Vol. F, ch. 16.1, pp. 421-422   | 1 | 2 |

Section 16.1.9.3. Recognizing solutions

G. M. Sheldrick,a C. J. Gilmore,b H. A. Hauptman,c C. M. Weeks,c* R. Millerc and I. Usónd

aLehrstuhl für Strukturchemie, Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany,bDepartment of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK,cHauptman–Woodward Medical Research Institute, Inc., 700 Ellicott Street, Buffalo, NY 14203–1102, USA, and dInstitució Catalana de Recerca i Estudis Avançats at IBMB-CSIC, Barcelona Science Park. Baldiri Reixach 15, 08028 Barcelona, Spain
Correspondence e-mail:  weeks@hwi.buffalo.edu

16.1.9.3. Recognizing solutions

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On account of the intensive nature of the computations involved, SnB and SHELXD are designed to run unattended for long periods while also providing ways for the user to check the status of jobs in progress. The progress of current SnB jobs can be followed by monitoring a figure-of-merit histogram for the trial structures that have been processed (Fig. 16.1.9.2[link]). A clear bimodal distribution of figure-of-merit values is a strong indication that a solution has, in fact, been found. However, not all solutions are so obvious, and it sometimes pays to inspect the best trial even when the histogram is unimodal. The course of a typical solution as a function of SnB cycle is contrasted with that of a nonsolution in Fig. 16.1.9.3[link]. Minimal-function values for a solution usually decrease abruptly over the course of just a few cycles, and a tool is provided within SnB that allows the user to visually inspect the trace of minimal-function values for the best trial completed so far. Fig. 16.1.9.3[link] shows that the abrupt decrease in minimal-function values corresponds to a simultaneous abrupt increase in the number of peaks close to true atomic positions. In this example, a second abrupt increase in correct peaks occurs when Fourier refinement is started.

[Figure 16.1.9.2]

Figure 16.1.9.2 | top | pdf |

A histogram of figure-of-merit values (minimal function) for 378 scorpion toxin II trials. This bimodal histogram suggests that ten trials are solutions.

[Figure 16.1.9.3]

Figure 16.1.9.3 | top | pdf |

Tracing the history of a solution and a nonsolution trial for scorpion toxin II as a function of Shake-and-Bake cycle. (a) Minimal-function figure of merit, and (b) number of peaks closer than 0.5 Å to true atomic positions. Simple peak picking (200 or 0.4Nu peaks) was used for 500 (Nu) cycles, and 500 peaks (Nu) were then selected for an additional 50 (0.1Nu) dual-space cycles. The solution (which had the lowest minimal-function value) was then subjected to 50 cycles of Fourier refinement.

Since the correlation coefficient is a relatively absolute figure of merit (given atomic resolution, values greater than 65% almost invariably correspond to correct solutions), it is usually clear when SHELXD has solved a structure, although when the data do not extend to atomic resolution the CC values are less informative, and for a substructure they depend strongly on the data quality.








































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