General guidelines for choosing values for the free parameters in the SINATRA Pro pipeline software.

The guidelines provided are based off of intuition gained through the simulation studies. In practice, we suggest specifying multiple cones c > 1 and utilizing multiple directions d per cone (see monotonically increasing power in S1 Fig in Supporting Information). While the other two parameters (θ and l) do not have monotonic properties, their effects on SINATRA’s performance still have natural interpretations. Selection of θ ∈ [0.1, 0.8] supports previous theoretical results that cones should be defined by directions in close proximity to each other [13, 15]; but not so close that they explain the same local information with little variation. Note that our sensitivity analyses suggest that the power of SINATRA Pro is relatively robust to the choice of θ. Optimal choice of l depends on the size of the protein molecules that are being analyzed. Intuitively, for rigid proteins, coarse filtrations with too few sublevel sets cause SINATRA Pro to miss or “step over” structural shifts that occur locally during the course of a molecular dynamic (MD) trajectory. In practice, we recommend choosing the angle between directions within cones θ and the number of sublevel sets l via cross validation or some grid-based search.