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Conclusions
Brunger, A. T., Adams, P. D., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Pannu, N. S., Read, R. J., Rice, L. M. and Simonson, T.  International Tables for Crystallography (2012). Vol. F, Section 18.6.10, p. 517 [ doi:10.1107/97809553602060000860 ]
Conclusions 18.6.10. Conclusions CNS is a general system for structure determination by X-ray crystallography and ... allows the novice to perform standard tasks. The interface provides a convenient means of editing complicated task files, even for the ... graphical output are planned in the future. Most operations within a crystallographic algorithm are defined through modules and task files. ...

Conclusions
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.8, p. 472 [ doi:10.1107/97809553602060000856 ]
... Simulated annealing has dramatically improved the efficiency of crystallographic refinement. A case in point is the combination of torsion-angle molecular ... Burling et al., 1996). Thus, simulated annealing is also a stepping stone towards development of improved models of macromolecules in ... review are implemented in the software suite Crystallography & NMR System (Brunger et al., 1998). A pre-release of the ...

Ensemble models
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.7, pp. 471-472 [ doi:10.1107/97809553602060000856 ]
... equation (18.2.3.1). Rather, the X-ray diffraction data represent a spatial and temporal average over all conformations that are assumed ... are simultaneously refined against the observed data, may thus be a more appropriate description of the diffraction data. This has been ... nger, 1994; Burling et al., 1996). An advantage of a multi-conformer model is that it directly incorporates many ...

Multi-start refinement and structure-factor averaging
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.6, p. 471 [ doi:10.1107/97809553602060000856 ]
... computer time is available, multi-start refinement has several advantages. A more optimal single model than that produced by a single simulated-annealing calculation can usually be obtained. Furthermore, each separate model coming from a multi-start refinement fits the data slightly differently. This ...

Examples
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.5, pp. 470-471 [ doi:10.1107/97809553602060000856 ]
... . In another realistic test case (Adams et al., 1999), a series of models for the aspartic proteinase penicillopepsin were generated ... among these structures ranged from 100% to 25%, thus providing a set of models with increasing coordinate error compared to the ... latter case, phases from single isomorphous replacement (SIR) were used. A very large number of conjugate-gradient cycles were carried ...

An intuitive explanation of simulated annealing
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.4.4, p. 470 [ doi:10.1107/97809553602060000856 ]
... any optimization problem is to find the global minimum of a target function. In the case of crystallographic refinement, one searches ... reasonable covalent and non-covalent interactions. Simulated-annealing refinement has a much larger radius of convergence than conjugate-gradient minimization (see below). It must, therefore, be able to find a lower minimum of the target E [equation (18.2.3.1)] than ...
     [more results from section 18.2.4 in volume F]

A priori chemical information
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.3.2, p. 468 [ doi:10.1107/97809553602060000856 ]
A priori chemical information 18.2.3.2. A priori chemical information The parameters for the covalent terms in ... derived from the average geometry and (r.m.s.) deviations observed in a small-molecule database. Extensive statistical analyses were undertaken for ...
     [more results from section 18.2.3 in volume F]

Cross validation
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.2, pp. 466-467 [ doi:10.1107/97809553602060000856 ]
... validation 18.2.2. Cross validation Cross validation (Brünger, 1992) plays a fundamental role in the maximum-likelihood target functions described below. A few remarks about this method are therefore warranted (for reviews ... cross validation, the diffraction data are divided into two sets: a large working set (usually comprising 90% of the data) ...

Introduction
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, Section 18.2.1, p. 466 [ doi:10.1107/97809553602060000856 ]
... formulated as the chemically constrained or restrained nonlinear optimization of a target function, which usually measures the agreement between observed diffraction ... of an atomic model with observed diffraction data and with a priori chemical information. The target function used for this optimization ... the number of atoms in the model) gives rise to a very complicated target function. This, in turn, produces what ...

Enhanced macromolecular refinement by simulated annealing
Brunger, A. T., Adams, P. D. and Rice, L. M.  International Tables for Crystallography (2012). Vol. F, ch. 18.2, pp. 466-473 [ doi:10.1107/97809553602060000856 ]
... formulated as the chemically constrained or restrained nonlinear optimization of a target function, which usually measures the agreement between observed diffraction ... of an atomic model with observed diffraction data and with a priori chemical information. Simulated annealing is an optimization technique particularly ... annealing can cross barriers between minima and thus can explore a greater volume of the parameter space to find better ...

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