VMD-L Mailing List

From: Mark Cunningham (cunningham_at_utpa.edu)
Date: Tue Jul 19 2011 - 11:53:54 CDT

 Maria:

The VMD licorice representation does exactly what you want, or at least
exactly what is shown in the figure you sent. To change the carbon color,
go to the Graphics..Colors menu. Select the Category Name and Name C,
then choose the color you want for carbon. If you select pink for carbon,
then VMD will draw a bond that is half pink and half blue (if connected to
nitrogen). If it is still somehow cyan, then you have TWO representations
that are drawing the bond. Delete the other representation.

Mark
________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of maria goranovic [mariagoranovic_at_gmail.com]
Sent: Tuesday, July 19, 2011 7:53 AM
To: VMD list
Subject: vmd-l: shades of licorice representation

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