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Moloc: Molecular Modelling on UNIX Workstations: 18 Conformational Libraries

Conformational Libraries

This menu provides tools to deal with conformation libraries. Such a library consists of a structure defined by its topology and a set of conformations. In addition, various properties may be attributed to a library (e.g. energy, radius of gyration), such that every conformation has a value attributed to each of those. Libraries are stored on disk in a non-ASCII format, but various public formats that contain structures with several conformations can be entered into Moloc and can be handled with the options of this menu. Most frequently libraries are used for united atom structures, but handling of C-alpha structures is also implemented.

18.1 Conformation Generator [generator]

Several methods (modes) to generate conformation libraries are provided. Most of these require typically much computation time, such that batch operation is recommended. Except for the trivial option n, one has to make sure to complete a set of specifications necessary for the chosen method before starting a conformation run (check on the menu items). This includes adjusting the parameters with the p option.

18.2 Fragment Positioning [positioning]

This menu serves to set up jobs to generate libraries of positioned fragments in a background environment. To start with, an entry (positions entry) must be created, the elements of which define the coordinate at which the fragments are initially (prior to energy minimization) placed. This is the purpose of the first few menu items. Option t sets thresholds relevant for some of these points, while option p addresses parameters relevant for the actual fragment positioning. Most points of this menu need be addressed to complete the setup of a positioning analysis.

18.3 Library Modifications [modify]

This menu provides various ways of modifying existing conformational libraries.

18.4 Library Data Generation [data]

For each specification made a new data field is introduced into the library which contains the corresponding value for each conformation. The user is informed on the text port about the name of the field and the range of values encountered.

The following options apply only to Calf libraries:

18.4.1 Examine Data

The conformational data associated with a library can be examined by several statistical methods. If non-graphical data are produced the program asks for a file name (default: standard output).

18.5 Library Analysis

Conformational libraries can be analyzed in various ways. In several cases the result is a subset of the library. Such subsets can be combined by logical operation to yield new subsets. Furthermore, a set can be yanked into a new library. Some of the menu items make only sense if subsets exist already.

18.6 Show Conformations

Several conformations from the libraries specified upon entering this menu can be displayed simultaneously in various colors. Initially only representatives are displayed. The conformations to be displayed can be selected according to various criteria.

18.7 Linking

This menu link fragments by linkers out of a library, A background entry can be given with which the linker can not intersect. A minimization with this background entry can be performed. All option are set by the p option or read in as a start up file (.Moloc) The result can be analyzed with the option a.

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