Q:
I’m analyzing protein structures (specifically, I’m performing a Voronoi-based analysis) using the tools linked on the geometry page:

http://geometry.molmovdb.org/NucProt/

I understand that the bisection of distances between atoms means that the radius does not matter. However, what happens at the boundary of the system?

Also, if you add ‘pseudo-water’ to the system, then do the water atoms need to have a particular radius? If not, then is there a distance cutoff?

A:
With respect to your first question (regarding the boundary of the system — ie the protein surface): the Voronoi volumes become large and potentially infinite. That’s why you need to introduce solvent. A course lecture may help to further explain this nicely:
http://www.gersteinlab.org/courses/452/09-spring/pdf/structure2.pdf

With respect to your second question (regarding the radius assigned to water): Yes, the water atoms most definitely need to have a particular radius. Distance cutoffs won’t work. You can probably use the normal water radius here.