From: McGuire, Kelly (
Date: Sun May 06 2018 - 23:34:32 CDT

Ok, I did wonder about that. Sometimes it seems PyMOL is more about the glitz and glamour, and VMD seems to be more scientifically professional. People ask me what I think of VMD vs PyMOL, and I usually tell them that VMD can do everything PyMOL can, but I like your response, because it is important to remember that just because you can do it, doesn't mean you should. Thanks!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

From: John Stone <>
Sent: Sunday, May 6, 2018 8:13:55 PM
To: McGuire, Kelly
Cc: VMD Mailing LIst
Subject: Re: vmd-l: Coloring Scheme Spectrum

  You can make VMD use any color scale you want, but before you run with
this and use a rainbow color scheme, you should first read this discussion
by Ken Moreland:

There are many discussions about choosing color maps well, but the
consensus in the visualization community is that many of
the most colorful "rainbow" style color maps have had a tendency to
cause more harm than good in terms of correct interpretation.

I attach an example script that emulates the built-in Matlab color
scales, but as I say above, you should think about what color scale
you want to use and why it's a good choice for whatever you're
trying to do.

  John Stone

On Sat, May 05, 2018 at 02:49:09PM +0000, McGuire, Kelly wrote:
> Wondering if the rainbow spectrum color scheme in PyMOL is possible in
> VMD? Looks like they use a python script so I'm guessing that is possible
> in VMD too. Here is the link:

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349