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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 ]
... facility is made for cross-validating statistical properties, such as R values (Brünger, 1992), values (Kleywegt & Brünger, 1996; Read, 1997) and maximum-likelihood functions (Pannu & Read, 1996; Adams et al., 1997). Similar operations exist ...

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 ]
... include the maximum-likelihood functions MLF, MLI and MLHL (Pannu & Read, 1996; Adams et al., 1997; Pannu et al., 1998). ... to recalculate the cross-validated error estimates (Kleywegt & Brunger, 1996; Read, 1997) and the weight between the X-ray diffraction target ... dynamics simulated annealing. References Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Cross- ...

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 ]
Modules and procedures 18.6.6. Modules and procedures Modules exist as 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 and ...

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 ]
... complicated maximum-likelihood target functions (Bricogne, 1984; Otwinowski, 1991; Pannu & Read, 1996; Pannu et al., 1998) can be defined using the ... language. For example, the maximum-likelihood target function MLF (Pannu & Read, 1996) and its derivative with respect to the calculated structure ... and `d' and are the cross-validated D and functions (Read, 1990; Kleywegt & Brünger, 1996; Read, 1997) which are ...

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 ]
... central facility in CNS. Fig. 18.6.4.1 shows how , and D (Read, 1986, 1990) are computed from the observed structure factors (`fobs ... with the same partitioning used for the test set. References Read, R. J. (1986). Improved Fourier coefficients for maps using ...

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 ]
... facility is made for cross-validating statistical properties, such as R values (Brünger, 1992), values (Kleywegt & Brünger, 1996; Read, 1997) and maximum-likelihood functions (Pannu & Read, 1996; Adams et al., 1997). Similar operations exist ...

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 ]
... Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, ...

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