VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon May 07 2018 - 09:47:44 CDT

That was very helpful Giacomo, thanks! I learned a lot about VMD at one of U of I's recent workshops, things I didn't even know could be done. Some people around me give VMD a bad wrap, believing that it can't do much and it's too hard to use. There biggest complaint was they thought PyMOL's graphics looked better, but I showed them that VMD could do almost exactly the same including the rainbow spectrum. But, John's comment seemed really important, that it's not just about making it look fancy.

Kelly L. McGuire
PhD Scholar
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602

________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Monday, May 7, 2018 6:33:02 AM
To: McGuire, Kelly
Cc: John Stone; VMD Mailing LIst
Subject: Re: vmd-l: Coloring Scheme Spectrum

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.

Giacomo

On Mon, May 7, 2018 at 12:34 AM, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> 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 <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>>
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:
  http://www.kennethmoreland.com/color-advice/BadColorMaps.pdf

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
  vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>

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:
>
> https://pymolwiki.org/index.php/Spectrum 

--
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801<https://maps.google.com/?q=of+Illinois,+405+N.+Mathews+Ave,+Urbana,+IL+61801&entry=gmail&source=g>
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin