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6.1.3 Other errors

In a continuation run the use of a corrupted save file or a file that is not a save file can lead to the error message ``Premature end of save file''. This will also happen if a save file from the program ``crna'' is used for continuation with ``lrna''.

When a long sequence is being folded in N best mode, the number of potential secondary structures might become too large for the sorting buffer, especially if the ``window size'' parameter (3.4) is small. The error message ``More than ??? basepairs in sort at (???,???)'' will appear. The first ??? refers to the current value of the ``sortmax'' parameter defined in the lin.inc and circ.inc files. This parameter should be doubled in size until this error message no longer occurs. If this error is not corrected, there is a risk of missing some valid suboptimal foldings.

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