From: Giacomo Fiorin (
Date: Mon May 07 2018 - 07:33:02 CDT

They are both well-established scientific codes.

PyMOL's original developer (tip: look his bio up) felt that there wasn't a
good open-source 3D software for structural biology and drug discovery.
Whether he thought that the VMD license was too restrictive or that it had
different technical requirements, for sure the two codes have a good chunk
of overlap but different focus. Note that VMD originally stands for
"Visual Molecular Dynamics". If you do information-based modeling more
often than physics-based you may find PyMOL extremely useful.

Most people don't have an opinion on one software vs. the other: if either
one wasn't useful, it wouldn't make the short list in the first place :-)
The list should actually be a little longer than that.


On Mon, May 7, 2018 at 12:34 AM, McGuire, Kelly <> wrote:

> 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
> Hi,
> 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.
> Best,
> 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
> <,+405+N.+Mathews+Ave,+Urbana,+IL+61801&entry=gmail&source=g>
> Phone: 217-244-3349

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD