From: Mark Cunningham (
Date: Tue Sep 06 2011 - 07:35:23 CDT


AND is a logical and does not mean "in addition to." WITHIN is another VMD keyword.
What you probably meant was

same residue as water within 3 of residue X Y

This will return all (whole) water molecules where any atom in the water is within 3 A of
the list of residues that you provided. There are, of course, other ways of defining cavities,
if that is your real goal. Most involve rolling a sphere over the protein surface.


From: [] On Behalf Of Hitesh Patel
Sent: Tuesday, September 06, 2011 4:21 AM
To: Filip Persson;
Subject: Re: vmd-l: define water cavity using atom selection in graphical representations window

Hello Filip,
use "or" instead of "and" between two residues X and Y.. like..

water and within 3 of (residue X or residue Y)

because there will be no intersection of residue X and Y.

Hitesh Patel

On Tue, Sep 6, 2011 at 10:08 AM, Filip Persson <<>> wrote:
I am trying to define a cavity in a protein using the atom selection command in VMD. I tried using

water and within 3 of (residue X and residue Y)

in the 'selected atoms-field' in the graphical representations window, but nothing happens. Changing the distance does not help, so obviously I must be doing something wrong here. Is it possible to define cavities in a way similar to the command above, or should I use any other type of selection command?