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CNS, a program system for structure-determination and refinement
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, ch. 18.6, pp. 512-519 [ doi:10.1107/97809553602060000860 ]
Chapter 18.6. CNS, a program system for structure-determination and refinement The Crystallography & NMR System (CNS) is described. 18.6.1. Introduction We have developed a new and advanced software system, the Crystallography & NMR System (CNS ... 1998). The goals of CNS are: (1) to create a flexible computational framework for exploration of new approaches to ...

Example: combined maximum-likelihood and simulated-annealing refinement
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 18.6.9, p. 517 [ doi:10.1107/97809553602060000860 ]
... Example: combined maximum-likelihood and simulated-annealing refinement CNS has a comprehensive task file for simulated-annealing refinement of crystal structures ... the geometric energy function (Brünger et al., 1989), refines a flat bulk solvent model (Jiang & Brünger, 1994) and an ... rate of cooling and length of the annealing scheme. For a review of simulated annealing in X-ray crystallography, see ...

HTML interface
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 18.6.8, pp. 516-517 [ doi:10.1107/97809553602060000860 ]
... HTML interface The HTML graphical interface uses HTML to create a high-level menu-driven environment for CNS (Fig. 18.6.8.1). ... Common Gateway Interface (CGI) conversion scripts are available that transform a task file into a form page and the edited form page back into ...

Task files
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 18.6.7, p. 516 [ doi:10.1107/97809553602060000860 ]
... any numerical task in X-ray crystallographic structure determination using a minimal set of `hard-wired' functions and routines. A list of the currently available crystallographic procedures and features is ... by ), and choice boxes (indicated by ). Fig. 18.6.7.2 shows a portion of the `define' section of a typical CNS ...

Modules and procedures
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 18.6.6, pp. 515-516 [ doi:10.1107/97809553602060000860 ]
... separate files and contain collections of CNS commands related to a particular task. In contrast, procedures can be defined and invoked from within any file. Modules and procedures share a similar parameter-passing mechanism for both input and output. Modules ... it possible to write programs in the CNS language in a manner similar to that of a computing language, such ...

Symbolic target function
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 18.6.5, pp. 514-515 [ doi:10.1107/97809553602060000860 ]
... functions is illustrated by two examples. In the first example, a target function is defined for simultaneous heavy-atom parameter refinement ... to the calculated structure factors are shown in Fig. 18.6.5.1(a). The derivatives of the target function with respect to ... target function (e.g. excluding outliers), and the `cvselection' statement specifies a subset of reflections to be used for cross-validation ( ...

Statistical functions
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 18.6.4, pp. 513-514 [ doi:10.1107/97809553602060000860 ]
Statistical functions 18.6.4. Statistical functions The CNS language contains a number of statistical operations, such as binwise averages and summations. The resolution bins are defined by a central facility in CNS. Fig. 18.6.4.1 shows how , and D ... weight. The averages are computed binwise, and the result for a particular bin is stored in all selected reflections belonging ...

Symbols and parameters
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 18.6.3, p. 513 [ doi:10.1107/97809553602060000860 ]
... CNS commands, numbers, strings or symbols. Symbols are denoted by a dollar sign ($), and parameters by an ampersand (&). Symbols and parameters may contain a single data element, or they may be a compound data structure of arbitrary complexity. The hierarchy of ...

The CNS language
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 18.6.2, pp. 512-513 [ doi:10.1107/97809553602060000860 ]
... exist for electron-density maps, e.g. is an example of a truncation operation: all map values less than 0.1 are set to 0. Atoms can be selected based on a number of atomic properties and descriptors, e.g. sets the B ... can be accomplished by the following CNS commands: which computes a map on a 1Ĺ grid by Fourier transformation of ...

Introduction
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 18.6.1, p. 512 [ doi:10.1107/97809553602060000860 ]
Introduction 18.6.1. Introduction We have developed a new and advanced software system, the Crystallography & NMR System (CNS ... 1998). The goals of CNS are: (1) to create a flexible computational framework for exploration of new approaches to structure ... these goals, algorithms were moved from the source code into a symbolic structure-determination language which represents a new concept ...

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