VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 06 2018 - 21:20:13 CDT

Here are a few more perspectives on color maps:
  https://blogs.egu.eu/divisions/gd/2017/08/23/the-rainbow-colour-map/

  https://bids.github.io/colormap/

  http://www.fabiocrameri.ch/visualisation.php

  http://medvis.org/2012/08/21/rainbow-colormaps-what-are-they-good-for-absolutely-nothing/

  https://www.mathworks.com/tagteam/81137_92238v00_RainbowColorMap_57312.pdf

  http://serialmentor.com/dataviz/color-pitfalls.html

Best,
  John Stone

On Sun, May 06, 2018 at 09:13:55PM -0500, John Stone wrote:
> 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
>
>
> 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/