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3.10 Main menu

At this point, a menu appears offering the user the option of adding auxiliary information to constrain or otherwise alter the folding. This will be dealt with in the next section. If no special features are being selected, or after they have been selected, the user should select item 8 to begin processing. There will be a pause, usually from several minutes to several hours, while the program computes the energy matrices needed for the folding. In a save run, excution terminates after this long pause, while in a regular run, the program continues on to produce output in ``N best'' mode, or to the energy dot plot in ``Sub-optimal plot'' mode (3.11). In a UNIX environment, program execution can be pushed into background mode at this stage. It is advisable to run the program in its own window shell. All run types can be run as batch processes, as long as the run mode is not ``Sub-optimal plot''. The auxiliary program, ``batgen'', discussed in (5.1), has been designed to facilitate batch runs.

Michael Zuker
Thu Nov 2 14:28:14 CST 1995