VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
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 akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy. -----Original Message----- From: "Andrew DeYoung" <adeyoung_at_andrew.cmu.edu> Sender: owner-vmd-l_at_ks.uiuc.edu Date: Fri, 29 Nov 2013 12:37:41 To: <vmd-l_at_ks.uiuc.edu> Subject: vmd-l: Why are all carbon atoms lumped into C in the Name category in the colors dialog? Hi, 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