From: Axel Kohlmeyer (
Date: Mon Oct 18 2010 - 12:11:55 CDT

hi steve,

On Mon, Oct 18, 2010 at 12:22 AM, Steve Jensen <> wrote:
> Hi Everyone!
> I use VMD for modeling molecules on surfaces and I want to create the
> illusion that a molecule is moving across the surface in a particular
> direction. (Imagine  a Star Trek warp speed kind of effect.)  I don't think
> that VMD would be able to do something like this so I wanted to try

actually, i _do_ think you can do this with VMD.
the tcl scripting in VMD is pretty powerful and you
can pick your molecule of choice with an atom
selection and then apply translations and rotations
to it to your liking. if you do this in a loop and add
a delay and display update to it, you can view the
resulting animation in VMD directly. if, however, you
want to render it into an mpeg or similar movie,
all you need is to add the suitable render command
and render/process/compress it as needed.

> exporting the data using vmd into something that Maya or some other program
> could handle.  Could anyone give a recommendation of the best way to start?

those kind of programs are typically not suited for the large
number of objects that typical molecular systems contain.

i have been thinking about how to do this for quite a while
(not so much to animate the molecules, but to add
objects to an existing visualization), but have not yet found
a good idea to make this easy and efficient.


> (what file formats are more universal would be a good start)  I saw in the
> manual that you can export for rendering, but I'm not so sure that this is
> what I want here since I need to modify it a bit.  Is there maybe a program
> that is easier to export to than maya for post image processing?
> Thanks for your help!
> Stephen

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