VMD-L Mailing List

From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Tue Jul 19 2011 - 10:10:01 CDT

You could simply overlay your licorice with VDW spheres for which you appropriately reduce the atom radii. Then your licorice can have one colour scheme, your VDW can have another.

B.

On 2011-07-19, at 8:53 AM, maria goranovic 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