VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jun 10 2021 - 13:26:26 CDT

On Thu, Jun 10, 2021 at 2:03 PM Chris Neale <candrewn_at_gmail.com> wrote:
[...]

>
> My actual use case is something like docking, where I want to view a
> "trajectory" with hundreds or thousands of frames that all have the same
> protein target but each frame has a different chemical bound, possibly in a
> different location, and certainly with different numbers/types of atoms in
> the small molecule component. I want them in the same molecule because
> activate/deactivate commands (or GUI) for different molecules is more
> cumbersome than pushing the frame slider along (though this makes me
> realize that just having a slider that activates/deactivates separate
> molecules in turn would do what I need after cloning a representation).
>

Have you looked at these two plugins?

https://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/
https://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/

They have been part of VMD for a very long time... Although "thousands of
frames" may be pushing the limit.

Axel.

> Thank you,
> Chris.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!tKBHhkKA4sDJiQM0uNMrr6SNvAFHfTHu0dTxxH0YrVZgQM5CL5jgQhx2DkXY5TColA$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.