BayesFold uses a natural approach to structure drawing, under which very few assumptions are made about the "correct" shape for a structure. For instance, BayesFold does not force all helices to connect to loops at right angles. BayesFold assumes only that loops are circular, that helices are rectangular, and that all bases are equally spaced,

These assumptions are applied uniformly everywhere in the structure, which means that parts of a structure that look similar are likely to actually be similar. Such a structure-drawing algorithm also conveys other information; for instance, the angle between adjacent stems on a loop corresponds to the proportion of loop bases that separates them.

However, this mimimal-assumption algorithm infrequently leads to sections of a structure overlapping each other in the structure drawing. Techniques for dealing with this occurrence are discussed in Section 2, “Handling Drawing Problems”.