Wayne K. Dawson
The linkage stem is consists of the stem first firming the pseudoknot in a given structure. This is expressed by the red regions of Figure 1 below. The linkage stem appears as the brackets in the secondary structure diagrams: for example, in an output that appears as the following, ((((((...[[[[[))))))...]]]]], the linkage stem corresponds to the '[' and ']' brackets.
When you chose a minimum stem length, that means that the program will ignore linkages that cannot in principle achieve at least this length. The purpose of this is to filter out excessive noise. If you know the linkage stem is 5 base pairs, you should not waste resource looking for linkage stems of length 4. Moreover, the stability of even a 4 base pair linkage stem is questionable. Finally, for such a large brush stroke program like vsfold, it is not very meaningful to ask for intimate details at the 2 Å scale. Structural considerations are worked into the vsfold's architecture, but not to such extreme detail.
Therefore, vsfold ignores potential linkage stems with lengths less that the minimum linkage stem length. The default value is 5 bps. By changing the value in the box, it can be increased or decreased accordingly.