From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Tue Jul 19 2011 - 08:52:19 CDT

I tried what axel suggests, using a licorice representation by color and a
vdw representation of non-carbon atoms by name (native colors, oxygen is red
for example). This works somewhat all right, but the non-carbon spheres
which are represented in their native color (color by name), appear as
little balls, and not as an extension of a bond as in a licorice
representation. Increasing the bond radius in licorice, or decreasing the
sphere size in the vdw representation completely hides the vdw
representation. The effect is not the same at all. Is there another way?

On Tue, Jul 19, 2011 at 3:44 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> maria,
>
> you can achieve what you describe by overlaying a "Bonds" representation
> with a "VDW" representation and using different coloring schemes and
> adjusting the radii of the respective representations accordingly.
>
> cheers,
> axel.
>
> On Tue, Jul 19, 2011 at 8:53 AM, maria goranovic
> <mariagoranovic_at_gmail.com> wrote:
> > Hi
> > I am wondering if this feature is already present in VMD?
> > In Pymol, it is possible to color an amino acid residue represented as
> > licorice in say, orange, and yet one can distinguish between different
> atoms
> > of the residue. For example, all bonds will become pink, but a nitrogen
> will
> > still appear blue and an oxygen red. If I try to color all carbons in VMD
> > pink, a C-N bond still appears in the cyan color, and the effect is not
> the
> > same.
> > Such a representation can be very useful in visualization. for example:
> > http://hwmaint.jbc.org/cgi/content/full/285/34/26245/F4
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

-- 
Maria G.
Technical University of Denmark
Copenhagen