From: Axel Kohlmeyer (
Date: Tue May 24 2011 - 14:08:26 CDT


i totally forgot to insert a plug (pun intended) here for the vmd debug plugin.

(sidenode: john, i just noticed that there is no working URL for the
vmddebug plugin documentation.)

On Tue, May 24, 2011 at 1:13 PM, John Stone <> wrote:
> Maria,
>  This is most likely an "atom selection leak", where your script is
> creating a large number of atom selections but not deleting them as
> it no longer needs them.  Make sure that you delete any atom selections
> that are being created as each frame is loaded, before the script moves
> on to process the next frame.

as of VMD 1.9 there is a plugin that can help tracking how many atom selections
you make and thus show you whether you have a "selection leak". it can even
help with narrowing down where the leak is. this makes use of some advanced
Tcl scripting features so i would love to hear, if this works for
everybody or if not
and where and how not.

the usage of the plugin is very simple.

package require vmddebug
debug atomselect on

and then run your code and with:

debug atomselect stats

you can get an update of how many selections have been
allocated. if you want to track individual atomselect invocations
and uses of the selection functions, you can do:

debug atomselect verbose

good luck,

> Cheers,
>  John Stone

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.