On rare occasions, BayesFold's structure drawing algorithm causes "collisions"-- overlapping between sections of a structure--as in the figure below:

BayesFold does not try to automatically correct collisions because such techniques tend to be both time-consuming and inaccurate. However, collisions can often be removed by varying one or more of the global settings for the structure drawing. These settings are accessible through the Formats tab, as discussed in Section 3, “Understanding the Format Palette”. Increasing the stem height is a good approach; it has the effect of increasing the angles between stems and, thus, "opening up" structures that fold in on themselves. Changing the stem height from 75 to 100 pixels successfully removes the collision in the example structure, as shown below.

Altering the nucleotide spacing setting can also help to correct collisions, especially when in conjunction with changing stem height. The figure below demonstrates the effect of reducing the nucleotide spacing from 50 to 42 pixels after applying the stem height change discussed above. The previously overlapped stems are now in no danger of colliding.

Future versions of BayesFold will allow users to correct collisions more directly, by manually dragging structure helices into new positions when a collision occurs.