International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

International Tables for Crystallography (2012). Vol. F, ch. 18.6, p. 513   | 1 | 2 |

Section 18.6.3. Symbols and parameters

A. T. Brunger,a* P. D. Adams,b W. L. DeLano,c P. Gros,d R. W. Grosse-Kunstleve,b J.-S. Jiang,e N. S. Pannu,f R. J. Read,g L. M. Riceh and T. Simonsoni

aHoward Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Stanford Synchrotron Radiation Laboratory (SSRL), Stanford University, 1201 Welch Road, MSLS P210, Stanford, CA 94305, USA,bThe Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA,cGraduate Group in Biophysics, Box 0448, University of California, San Francisco, CA 94143, USA,dCrystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands,eProtein Data Bank, Biology Department, Brookhaven National Laboratory, Upton, NY 11973–5000, USA,fDepartment of Mathematical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2G1,gDepartment of Haematology, University of Cambridge, Wellcome Trust Centre for Molecular Mechanisms in Disease, CIMR, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, England,hDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA, and iLaboratoire de Biologie Structurale (CNRS), IGBMC, 1 rue Laurent Fries, 67404 Illkirch (CU de Strasbourg), France
Correspondence e-mail:  brunger@stanford.edu

18.6.3. Symbols and parameters

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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 of CNS commands, numbers, strings or symbols.

Symbols are denoted by a dollar sign ($), and parameters by an ampersand (&). Symbols and parameters may contain a single data element, or they may be a compound data structure of arbitrary complexity. The hierarchy of these data structures is denoted using a period (.). Figs. 18.6.3.1(a)[link] and (b)[link] demonstrate how crystal-lattice information can be stored in compound symbols and parameters, respectively. The information stored in symbols or parameters can be retrieved by simply referring to them within a CNS command: the symbol or parameter name is substituted by its content. Symbol substitution of portions of the compound names (e.g. `&crystal_lattice.unit_cell.$para') allows one to carry out conditional and iterative operations on data structures, such as matrix multiplication.

[Figure 18.6.3.1]

Figure 18.6.3.1 | top | pdf |

Examples of compound symbols and compound parameters. (a) The `evaluate' statement is used to define typed symbols (strings, numbers and logicals). Symbol names are in bold. (b) The `define' statement is used to define untyped parameters. Each parameter entry is terminated by a semicolon. The compound base name `crystal_lattice' has a number of sub-levels, such as `space_group' and the `unit_cell' parameters. `unit_cell' is itself base to a number of sub-levels, such as `a' and `alpha'. Parameter names are in bold.








































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