VMD-L Mailing List

From: Fred Moore (moore_at_whitman.edu)
Date: Fri Mar 23 2007 - 13:24:37 CDT

Greetings from a newbie to VMD.

I'm running the latest version on a macintosh pb 12" powerpc with the
latest osx.

I'm trying to view and animate a .pdb file full of chloroform
molecules. The .pdb file names the atoms in each molecule:

C1, CL1, CL2, CL3, H

Those names show up properly when I go to Graphics->Representations
and look under "keyword". The values are: C1, CL1, CL2, CL3, H

I'd like to be able to color those atoms differently. The default
coloring has the Hydrogen as white, and this is what the:

Graphics->Colors...

menu shows. However the names menu under

Graphics->Colors...

doesn't show these (C1, CL1, CL2, CL3, H) names and the only one that
I seem to be able to control is "H". As far as the Color Controls
menu is concerned
C1, CL1, CL2, CL3 are all the same name and it colors them uniformly.

Is this behavior normal?

If so, is there a menu based way to color my atoms ((C1, CL1, CL2,
CL3, H) differently?

thanks in advance!

Fred M.