VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Mar 16 2018 - 10:10:31 CDT

There isn't a mathematically unique solution, because you have a 3D density
map that gradually goes to zero.

But to could probably use the volutil command in VMD (package require
volutil):
1. use the -clamp option to set to zero all the values of the map that are
below a certain threshold;
2. use the -binmask option to generate a binary mask of the resulting map.

volutil doesn't seem to have an option to compute the integral of a map,
but it shouldn't be difficult to open the masked map in another script (a
.dx is a text file with comments at the top) and just count the 1's and 0's--94eb2c075f18c577d305678904dc--