From: Florian Barth (
Date: Wed Mar 10 2004 - 07:10:27 CST


I have done some protein-ligand dockings and I'm using vmd 1.8.2/linux
to visualize the docked ligand conformations (trajectory pdb format). I
would like to color the conformers by docking energy and therefore I
have inserted the energy value for each into the occupancy field of the
pdb file. Of course, the energy is the same for every atom of one
confomer, there are only changes between different conformations. But it
appears that vmd normalizes the values for each molecule, because all
molecules have the same color when using the occupancy coloring method.
Is there any way have the molecules colored according to predefined
(floating-point-)values in the pdb file?


        Florian Barth