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

International Tables for Crystallography (2006). Vol. F, ch. 25.2, p. 715   | 1 | 2 |

Section 25.2.3.7. Task files

A. T. Brunger,v* P. D. Adams,e W. L. DeLano,f P. Gros,g R. W. Grosse-Kunstleve,e J.-S. Jiang,h N. S. Pannu,i R. J. Read,j L. M. Ricek and T. Simonsonl

25.2.3.7. 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. 25.2.3.7[link].

[Figure 25.2.3.7]

Figure 25.2.3.7 | 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. 25.2.3.8[link] shows a portion of the `define' section of a typical CNS refinement task file.

[Figure 25.2.3.8]

Figure 25.2.3.8 | 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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