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getting the center of mass of each part of a molecule

Dear Gregory Ewing,

As I said before, I need to divide the molecule into two parts but don't know how to do it? It seems that I need to choose/determine a plane in 3D space which cuts the molecule in two parts. As John Ladasky suggested, I need to describe the criteria that cut needs to satisfy as well. Could you please tell me on the code how to do those steps?