From: Alex Hummels (
Date: Thu Aug 08 2019 - 09:28:30 CDT


I’m currently working with diffusion of water within a certain distance of a protein and I was wanting to know more in depth how the “within” command works. Specifically, if I make a selection like

set sel [atomselect top “name OH2 and (within 5 of protein)”]

does the within command determine which Oxygen atoms are within 5 Å by measuring the distance from each protein atom? Or is it something more complex like measuring the shortest distance which is perpendicular to the protein surface?

If anyone knows the answer or knows where to point me to source code where I could find out myself that would be wonderful.