VMD-L Mailing List

From: Brooke Dallas (bdallas_at_ucdavis.edu)
Date: Wed Oct 13 2010 - 11:31:16 CDT

Thanks Axel,

The molecule has 38 atoms and it only needs to be a static image.

Brooke

On Wed, Oct 13, 2010 at 3:41 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, 2010-10-13 at 14:46 +0100, Brooke Dallas wrote:
> > Dear Vmd List,
>
> dear brooke,
>
> > I need to draw a molecule with bond colors indicating the RMS bond
> > length fluctuation for each bond, e.g. blue for small RMS fluctuations
> > continuous to red for large RMS fluctuations. Does anybody have any
> > suggestions for how to do that?
>
> how large a molecule?
> does it have to be dynamics or only a static image?
>
> VMD doesn't have any internal provisions for things like this,
> so you would either have to do some kind of hack with multiple
> representations, or draw the bonds manually from a script.
>
> if you can give some more details about what you want to
> achieve and for what purpose you need this, somebody may
> be able to come up with some suggestions for doing this.
>
> cheers,
> axel.
>
> > Thanks in advance,
> >
> > Brooke Dallas
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>