VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
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:
https://urldefense.com/v3/__http://www.theochem.ruhr-uni-bochum.de/*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.
http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/
to replicate the visualization from one molecule to others there is a tool
as well: https://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/

These also go back a long time...

On Thu, Sep 2, 2021 at 12:03 PM Prof. Eddie <eackad_at_siue.edu> 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
> <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!rNcESRGlDZgdxgCsQ6-XA-4kzihjRC6hYzZDY84ytPVlaSB3CHh9DLjpUvOPBO1axQ$>
> Associate Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!s2rJqUZioWPZRQA8gzKQJ-aTjRq2G-19ZliT_SBCTkFxfvSqIQWmkxRh-haMsf2ATg$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.