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6.1.2 Printer output error

The message ``Base pair between ??? and ??? conflicts with at least one other pair'' signals that the printer output subroutine (linout) has detected a pseudoknot in a secondary structure. This happens when two base pairs r<sub>i</sub>-r<sub>j</sub> and r<sub>i′</sub>-r<sub>j′</sub> are detected with i < i′ < j < j′ This should not occur using lrna or crna, but might occur when the program ``efn'' is run, since an artificially created ct file could contain a knotted structure.

The message ``Buffer overflow in lineout'' indicates that a very long helix has been found that overflows the output buffer in the linout subroutine (in mrna.f or mrna1.f). The solution is to increase the second dimension of the ``array'' variable, as well as the value of the ``amax'' variable, to a common number larger than 900.

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