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3.11.3 Computing structures

Once a base pair has been selected, the best folding containing that base pair can be computed by selecting the ``Compute structure for last (i,j)'' (IRIS), or ``Compute structure'' (X11) option from the popup menu. The computed structure will only be sent to the output files if at least ``window size'' new base pair occur that are not in or too near base pairs that have already been found in computed structures. The base pairs in and within a distance of ``window size'' of the computed structure will be marked and will not appear in the dot plot when it is redrawn.

If one wishes to compute secondary structures in this mode, it is advisable to send them to a file, rather than to the ``terminal''. In the latter case, the output will be sent to the window that called the program. This window is resized and hidden in the IRIS version, although it can be displayed using the ``Toggle textport'' option from the popup menu.

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