From: Axel Kohlmeyer (
Date: Thu Sep 02 2021 - 11:14:40 CDT

In VMD graphics are associated with the "molecule" and not with the
"trajectory frame".

so you would need to do some smart scripting that enables/disables the
desired graphics object for a given frame.
I have worked out and example for that using some quantum chemistry
software a looooong time ago (like > 15 years ago).
You can still see that on the "historic" webpages from that time:*legacy.akohlmey/cpmd-vmd/part5.html*chap7_sect6__;fiM!!DZ3fjg!s2rJqUZioWPZRQA8gzKQJ-aTjRq2G-19ZliT_SBCTkFxfvSqIQWmkxRh-hZdtkLxOg$

An alternative would be to create a visualization with one trajectory frame
and one graphics file into a new molecule for each frame and then toggle
between the frames.
to replicate the visualization from one molecule to others there is a tool
as well:

These also go back a long time...

On Thu, Sep 2, 2021 at 12:03 PM Prof. Eddie <> wrote:

> Hi all,
> For our trajectories, we've created a 3d ply visualization for each frame.
> That is, each frame has an associated ply file. When loading ply files into
> vmd, it seems they do not stack (or if they do I couldn't get them to).
> What I'd like is to have two vmd mols, one for the trajectory (dcd
> structure) and one for the 3d structures so when animated, both a
> synchronized. Is there any way we can do this with the ply files?
> Thanks,
> Eddie
> --
> _________________________________________________________
> Edward Ackad, Ph.D
> <*7Eeackad__;JQ!!DZ3fjg!rNcESRGlDZgdxgCsQ6-XA-4kzihjRC6hYzZDY84ytPVlaSB3CHh9DLjpUvOPBO1axQ$>
> Associate Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390

Dr. Axel Kohlmeyer;!!DZ3fjg!s2rJqUZioWPZRQA8gzKQJ-aTjRq2G-19ZliT_SBCTkFxfvSqIQWmkxRh-haMsf2ATg$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.