[Chimera-users] [chimerax-users] Color palettes - ColorBrewer support?

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 12 13:47:21 PDT 2017

Hi Oli and everybody else,

In the ChimeraX daily build, the ColorBrewer palettes are available with “rainbow” (aka “color sequential”) and with the “color” command “map” option.  The latter is the functional equivalent of Chimera’s “scolor” command, coloring by map value.  

I realize documentation is needed since the ColorBrewer website doesn’t show the names of the palettes.  I plan to have this done today, to be available tomorrow on the website and in the daily build.  For now, 3 important notes:

(1) anybody eager to try today can use Chimera to discover the names that could be used in the ChimeraX command line (start Chimera, enter command “start Palette Editor”, choose any relevant options and click the palette of interest)

(2) users should cite: www.ColorBrewer.org, color specifications and designs by Cynthia A. Brewer, Pennsylvania State University.

(3) currently if coloring by map value, you cannot control the exact value-color mapping with palettes from colorbrewer or colourlovers; the colors in the palette are spaced equally along the range of values.

They are quite fun to play with, as I’ve been doing today.
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 10, 2017, at 7:57 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> Hi Conrad that’s fantastic, thanks! The only other case I can think of off hand would be scolor for coloring maps e.g. by local resolution.
> Cheers
> Oli
> On 9/10/17, 2:52 AM, "Conrad Huang" <conrad at cgl.ucsf.edu> wrote:
>    I wrote some code to add colorbrewer schemes as colormap (palette) 
>    names, so they should be available with the "color" and "rainbow" 
>    commands (in tomorrow's daily build).  Those were the most obvious uses. 
>      What are others?  If they are easy, we can drop them in.
>    Conrad

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