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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 ]
... Kleywegt & Brünger, 1996; Read, 1997) and maximum-likelihood functions (Pannu & Read, 1996; Adams et al., 1997). Similar operations exist ... even complicated maximum-likelihood target functions (Bricogne, 1984; Otwinowski, 1991; Pannu & Read, 1996; Pannu et al., 1998) can be defined using the CNS ...

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 ]
... functions include the maximum-likelihood functions MLF, MLI and MLHL (Pannu & Read, 1996; Adams et al., 1997; Pannu et al., 1998). The user can choose between slow ... also after molecular-dynamics simulated annealing. References Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. ( ...

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 18.6.8. HTML interface The HTML graphical interface uses HTML to create a high-level menu-driven environment for CNS (Fig. 18.6.8.1). Compact and relatively simple Common Gateway Interface (CGI) conversion scripts are available that transform a task file into a form page and the edited form page back ...

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 ]
Task files 18.6.7. Task files Task files consist of CNS language statements and module invocations. The CNS language permits the design and execution of nearly 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 ...

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 ]
... parameter and topology databases. References Blundell, T. L. & Johnson, L. N. (1976). Protein Crystallography, pp. 375-377. London: Academic Press. ...

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 ]
... even complicated maximum-likelihood target functions (Bricogne, 1984; Otwinowski, 1991; Pannu & Read, 1996; Pannu et al., 1998) can be defined using the CNS language. ... CNS language. For example, the maximum-likelihood target function MLF (Pannu & Read, 1996) and its derivative with respect to the ...

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 (Read, 1986, 1990) are computed from the observed structure factors (`fobs') and the calculated ...

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 ]
Symbols and parameters 18.6.3. Symbols and parameters The CNS language supports two types of data elements which may be used to store and retrieve information. Symbols are typed variables, such as numbers, character strings of restricted length and logicals. Parameters are untyped data elements of arbitrary length that may contain collections ...

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 ]
... Kleywegt & Brünger, 1996; Read, 1997) and maximum-likelihood functions (Pannu & Read, 1996; Adams et al., 1997). Similar operations exist ... diffraction data to space group P1. References Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997) ...

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 ]
... W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & ...

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