[Chimera-users] creating a new color palette - viridis

[Elaine Meng]

Hi Shyam,
That message was about adding palettes to ChimeraX, not Chimera.  

Chimera has had Colorbrewer palettes for a long time, and although you can create your own custom palettes using the Palette Editor, 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/palette.html>

 ... they are NOT very useful since the only way to use them is as a background gradient.  The longer-term goal was to allow using palettes for coloring by value (like bfactor) or sequentially (like N- to C-terminus of a chain), but it was never implemented.

Instead you can specify a series of colors directly in the command “rangecolor” (for coloring by value) or “rainbow” (for coloring sequentially), or choose colors in the corresponding tool GUIs: Color by Attribute or Rainbow.

Viridis looks something like dark blue -> green -> yellow or gold, so you could try something like Chimera command:

rainbow midnightblue,blue,green,gold

(you can experiment with what and how many colors are used; it’s not limited to Chimera named colors, e.g. you could also use hex codes)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html#colorname>

In ChimeraX, with the “color” command you can use predefined palettes or specify the series of colors directly in the command.  ChimeraX does not have rainbow or color-by-attribute GUIs yet.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html>

In ChimeraX, the command would be something like:

rainbow palette midnightblue:blue:green:gold

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 22, 2019, at 10:03 AM, Saladi, Shyam M. <saladi at caltech.edu> wrote:
> 
> Hello --
> I see that a number of color palettes were added to chimera a little more than a year ago now:
> 
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-September/013872.html
> 
> I would like to try using viridis (https://bids.github.io/colormap/) instead of standard rainbow/spectrum for coloring a protein from its N to C termini. Would someone be able to give me direction on how to create a new a color palette to do this? 
> 
> The RGB values making up viridis can directly be found here: here: https://github.com/BIDS/colormap/blob/master/colormaps.py 
> 
> Thanks,
> Shyam