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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 ]
... selections are possible, e.g. selects all reflections with Bragg spacing, d, greater than 3 Ĺ for which both native (fp) and derivative ... 1996; Read, 1997) and maximum-likelihood functions (Pannu & Read, 1996; Adams et al., 1997). Similar operations exist for electron-density ... a central facility in CNS. Fig. 18.6.4.1 shows how , and D (Read, 1986, 1990) are computed from the observed structure ...

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 ]
... maximum-likelihood functions MLF, MLI and MLHL (Pannu & Read, 1996; Adams et al., 1997; Pannu et al., 1998). The user ... the geometric energy function in the course of the refinement (Adams et al., 1997). This is important for the maximum ... energy minimization, and also after molecular-dynamics simulated annealing. References Adams, P. D., Pannu, N. S., Read, R. J. & Brü ...

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 ]
... International Tables for Crystallography (2012). Vol. F, ch. 18.6, p. 516 © International Union of Crystallography 2012 | home | resources | advanced search ...

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 ]
... H. & Jensen, L. H. (1989). X-ray Structure Determination, p. 33. New York: Wiley Interscience. International Tables for Crystallography (2012 ...

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 ]
... the structure-factor array for a bulk solvent model, and `d' and are the cross-validated D and functions (Read, 1990; Kleywegt & Brünger, 1996; Read, 1997 ... between different heavy-atom derivatives (Read, 1994). References Blow, D. M. & Crick, F. H. C. (1959). The treatment ...

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 ]
... a central facility in CNS. Fig. 18.6.4.1 shows how , and D (Read, 1986, 1990) are computed from the observed structure factors ... parameters are computed in binwise resolution shells. The (`sigmaD') and D parameters are then computed from and binwise averages involving and ...

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 ]
... International Tables for Crystallography (2012). Vol. F, ch. 18.6, p. 513 © International Union of Crystallography 2012 | home | resources | advanced search ...

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 ]
... selections are possible, e.g. selects all reflections with Bragg spacing, d, greater than 3 Ĺ for which both native (fp) and derivative ... 1996; Read, 1997) and maximum-likelihood functions (Pannu & Read, 1996; Adams et al., 1997). Similar operations exist for electron-density ... expansion of the diffraction data to space group P1. References Adams, P. D., Pannu, N. S., Read, R. J. & Brü ...

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 ]
... operations and `hard-wired' algorithms. References Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse- ...

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