From: Axel Kohlmeyer (
Date: Fri Nov 29 2013 - 19:13:50 CST

This is a design choice of vmd dating back to the origins of the program.

There are two approaches how you can address your issue:
You can assign different types to the atoms that you want to color differently and choose them so their first letters are different. This can be automated with a little script and then you can color by type.

Or you can make separate reprentations and overlay it with a representation for the connectivity.


Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.
-----Original Message-----
From: "Andrew DeYoung" <>
Date: Fri, 29 Nov 2013 12:37:41 
To: <>
Subject: vmd-l: Why are all carbon atoms lumped into C in the Name category in the colors dialog?
I have loaded a Gromacs .g96 file into VMD.  In my .g96 file, I have several
atom names that start with the letter C: CR, CW, CE, and so on.  All of
these atoms are carbons, but I would like to color them separately. 
However, when I go to Graphics -> Colors... and click on the Name category
in the dialog box that appears, I only see a single entry for carbon (i.e.,
"C"), rather than separate entries for CR, CW, CE, and so on.  
Is there any way I can specify separate colors for CR, CW, CE, and so on,
even though they are all carbons?
I could make separate representations for each of CR, CW, and CE and use the
"ColorID" Coloring Method in Graphical Representations, but if I did that, I
would lose the connectivity of the atoms (at least from my experience).
Thanks so much!
Andrew DeYoung
Carnegie Mellon University