From: Axel Kohlmeyer (
Date: Sun Feb 20 2011 - 12:18:56 CST

On Sat, Feb 19, 2011 at 5:33 PM, Iman Salehinia <> wrote:
> Dear friends,
> Is it possible to select atoms which are already labeled by picking from the
> VMD display? After that, I want to save the coordinates of the selected
> atoms which I know how to do that.

labeling atoms on the screen and the atom select command are two completely
different entities, so - to the best of my knowledge - there is no
direct way to do
that after the fact. however, VMD you can write script code that is triggered by
clicking on atoms and would then record the selected atoms and allow to write
them out.

the poor man's version of this would be to log the vmd console output and
look up the atom indices and build the selection based on index manually.


> Thanks,
> Iman.

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