VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Jul 31 2006 - 09:05:16 CDT

Hi Adrian,
a version of "Pos" coloring that behaves as you have described is
currently in the planning stages and should be included with a future
release, but isn't currently available. If you'd like to have this
coloring now, you should probably figure out what you want your coloring
function to be and map it to the beta field (let me know if this doesn't
make sense).

As far as color bands, please check out the color scale bar plugin
(http://www.ks.uiuc.edu/Research/vmd/plugins/colorscalebar/) and
remember that you can tweak the color scale data range under the
Trajectory tab of the graphical reps menu.

Best,
Peter

Adrian Koh wrote:
> Hi,
>
> Would it be possible to twitch the definition of existing coloring
> methods? For instance, the "Pos" is based on the distance of each
> atom to the center of the molecule. Say, if I have a molecular
> structure that takes on a cylindrical shape, could I define an
> alternative "Pos" based on the distance of each atom to the central
> axis instead?
>
> Also, would it be possible to display a legend for the color bands
> used for "Pos", so that one could know the specific magnitude of the
> distance the color represents?
>
> Thank you very much.
>
>
> Best Regards,
> Adrian.
>
>
>