From: Ellis, Matthew (
Date: Sat Feb 02 2019 - 04:38:32 CST


I have some code to visualise the output of a charge transfer simulation which uses VMD to plot xyz files (for atoms and molecules) and cube files to visualise the orbitals. The orbitals are in general complex and I would like to be able to visualise the phase of these with a color map (i.e. mostly real-positive would be reddish, mostly imaginary-negative would be greenish etc...). I have the relevant color map to map a complex number to a color. However, I do not know how to set the individual isosurfaces to specific colors.

I have tried setting the color of the isosurfaces via the 32 pre-defined colors. However, I soon run out of these. This also messes up the colors of other parts of the visualisation such as the background color. I understand that VMD has the capability to set up to 1024 user-defined colors? However, for the life of me I can't figure out how to use them to set isosurface colors!

Any help would be greatly appreciated,