Apart from selecting atoms, users must also specify a cutoff distance for clustering. This distance determines whether two molecules belong to the same cluster. The cutoff distance might be obtained from the radial distribution function (RDF) of the selected atoms (either the position of the RDF maximum or first minimum). The lack of a single clear choice for the cutoff distance is caused by the complex structures of self-assembled structures compared to, for examples, ions in solutions (i.e., the system is inherently not well-mixed). It is necessary to consider a range of cutoff distances, in our experience typically investigating a range of cutoffs between 8 Å and 13 Å is useful. Visual inspection of the resulting clusters determines the most appropriate cutoff distance straightforwardly in most cases. As well as soft matter, the SCP algorithm can be readily applied to biological systems, highlighting its broad applicability. For example, Figure shows the result of applying the SCP algorithm to a coarse-grained protein simulation to measure the aggregation of the transmembrane domains of a protein within a lipid bilayer.