VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 19 2011 - 08:44:13 CDT

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.