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3.3 Run mode selection

The menu :

             Enter run mode
0 Sub-optimal plot (default)
1 N best
2 Multiple molecules
is displayed.

If the Sub-optimal choice is selected, then the energy dot plot will be displayed on the screen and the user will be able to interact with it. Program execution continues with energy dot plot parameter selection (3.4).

In the ``N best'' mode, the program will compute a selection of optimal and suboptimal foldings sorted by energy. If the ``Multiple molecules'' mode is selected, the program will run in the ``N best'' mode for every complete sequence in the input sequence file. This last option can only be selected in the regular run mode. The aim here is to fold many sequences that are contained in a single input file. It is less cumbersome than folding each sequence separately. In the ``N best'' mode, program execution continues with ``N best'' parameter selection (3.5), while in ``Multiple molecules'' mode, the user is first prompted for a sequence file name (3.6).

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