Q:

Regarding your paper entitled "3V: cavity, channel and cleft

volume calculator and extractor", which I read carefully.

I’ve a question for you. In the abstract, it is written the following:

"It rapidly finds internal volumes by taking the difference between

two rolling-probe solvent-excluded surfaces,…", but I think you

mean "two imaginary rolling-probe solvent-excluded surfaces" because

after looking at your code, I haven’t seen any analytic SES

formulation therein. I guess you are just using two probe spheres of

distinct radii to account for cavities, not the analytic SES

themselves. Am I right?

A:

I am not certain about your use of the term "imaginary", but I would say my method is a "discrete approximation" to the SES. And because it is discrete (i.e. a 3D grid) one can simply subtract one grid from another. See attached figures.

With small grid sizes (0.2 A), I see very little discrepancy to the analytical solution.