Hi, The nearest neighbours are defined according to RMSD between the structures. If M=10, a new conformation x is added to a given cluster when a conformation y in the cluster exists such that: (1) x and y are neighbours, i.e., x has y among the 10 conformations with minimal RMSD to x and vice versa for y. (2) x any y have at least P (default: 3) neighbours in common.
You may want to prepare a diagram to graphically illustrate this. Ran Marc Charendoff wrote: > Hello, > > In the Jarvis-Patrick method g_cluster shows that when M=0, the > cutoff is used to determine nearest neighbors (those within X.X nm). > In the absence of cutoff - e.g. M is defaulted to 10, how are nearest > neighbors determined? What does M=10 (or anyother number) mean? > > Thanks, Marc
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