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. 516   | 1 | 2 |

Section 18.6.7. Task files

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

18.6.7. Task files

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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 procedures and features is shown in Fig. 18.6.7.1[link].

[Figure 18.6.7.1]

Figure 18.6.7.1 | top | pdf |

Procedures and features available in CNS for structure determination by X-ray crystallography.

Each task file is divided into two main sections: the initial parameter definition and the main body of the task file. The definition section contains definitions of all CNS parameters that are used in the main body of the task file. Modification of the main body of the file is not required, but may be done by experienced users in order to experiment with new algorithms. The definition section also contains the directives that specify specific HTML features, e.g. text comments (indicated by [\{^{*} \ldots ^{*}\}]), user-modifiable fields (indicated by [\{===\gt \}]), and choice boxes (indicated by [\{+ \hbox{ choice: } \ldots + \}]). Fig. 18.6.7.2[link] shows a portion of the `define' section of a typical CNS refinement task file.

[Figure 18.6.7.2]

Figure 18.6.7.2 | top | pdf |

Example of a typical CNS task file: a section of the top portion of the simulated-annealing refinement protocol which contains the definition of various parameters that are needed in the main body of the task file. Each parameter is indicated by a name, an equal sign and an arbitrary sequence of characters terminated by a semicolon (e.g. `a=61.76;'). The top portion of each task file also contains commands for the HTML interface embedded in comment fields (indicated by braces, [\{ \ldots \}]). The commands that can be modified by the user in the HTML form are in bold.

The task files produce a number of output files (e.g. coordinate, reflection, graphing and analysis files). Comprehensive information about input parameters and results of the task are provided in these output files. In this way, the majority of the information required to reproduce the structure determination is kept with the results. Analysis data are often given in simple columns and rows of numbers. These data files can be used for graphing, for example, by using commonly available spreadsheet programs. An HTML graphical output feature for CNS which makes use of these analysis files is planned. In addition, list files are often produced that contain a synopsis of the calculation.








































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