getting the center of mass of each part of a molecule

[jladasky at itu.edu]

On Thursday, May 18, 2017 at 1:43:20 PM UTC-7, qasi... at gmail.com wrote:
> 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?

You define the criteria, and then you write the code.

In your original post, you wrote: "The atoms of the first part/half according to the main COM of the ligand are C2, C7, C8 and C9. As for the second part they are C3, C4, C5 and C6 atoms."

HOW did YOU make that decision?  That's what you need to specify in order to write code.