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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 ]
... D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Cross-validated maximum likelihood enhances crystallographic simulated annealing ... the isomorphous replacement method. Acta Cryst. 12, 794-802. Blundell, T. L. & Johnson, L. N. (1976). Protein Crystallography, pp. 375 ... direct methods. Acta Cryst. A40, 410-445. Brünger, A. T. (1988). Crystallographic refinement by simulated annealing: application 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 ]
... D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Cross-validated maximum likelihood enhances crystallographic simulated annealing ... Natl Acad. Sci. USA, 94, 5018-5023. Brünger, A. T. (1988). Crystallographic refinement by simulated annealing: application to a ... aminotransferase. J. Mol. Biol. 203, 803-816. Brünger, A. T., Adams, P. D. & Rice, L. M. (1997). New ...

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 ]
... scattering components, and molecular parameter and topology databases. References Blundell, T. L. & Johnson, L. N. (1976). Protein Crystallography, pp. 375 ...

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 ]
... direct methods. Acta Cryst. A40, 410-445. Brünger, A. T. (1992). Free R value: a novel statistical quantity for ... of crystal structures. Nature (London), 355, 472-475. Burling, F. T., Weis, W. I., Flaherty, K. M. & Brünger, A. T. (1996). Direct observation of protein solvation and discrete ...

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 ]
... D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Cross-validated maximum likelihood enhances crystallographic simulated annealing ... refinement. Proc. Natl Acad. Sci. USA, 94, 5018-5023. Blundell, T. L. & Johnson, L. N. (1976). Protein Crystallography, pp. 375-377. London: Academic Press. Brünger, A. T. (1992). Free R value: a novel statistical quantity ...

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 ]
... data operations and `hard-wired' algorithms. References Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros ... M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Crystallography & NMR System (CNS): ...

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