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

Conrad Huang conrad at cgl.ucsf.edu
Sat Sep 9 23:52:39 PDT 2017


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

On 9/8/2017 1:20 PM, Elaine Meng wrote:
> HI Oli,
> Thanks for the suggestion. I agree these would be great to have in ChimeraX, and we certainly haven’t ruled it out… but (as you know) many things are vying for developer time.  I would certainly use those palettes if they were available.
> 
> We’re aware of Colorbrewer and actually its palettes have been in Chimera’s Palette Editor for quite a while:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/palette.html>
> 
> However, they never got interfaced with coloring by value and the only direct use was for gradient-coloring the background… admittedly not the best use of most multicolor schemes.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Sep 8, 2017, at 8:35 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>>
>> Hi,
>>   
>> I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)?
>>   
>> It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc.
>>   
>> It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet.
>>   
>> Cheers
>> Oli
>>   
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