[Chimera-users] Use of custom color palettes for Render by attribute?

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 14 13:03:27 PDT 2016


Hi Oliver,
In Chimera, the easiest way to repeatedly use some custom colormapping is with the “rangecolor” command… I know you’re quite expert with Chimera, but for everyone’s benefit, the manpage with examples is here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>

…and there are more examples in various tutorials, including:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

ChimeraX is not yet available and is changing rapidly.  Currently most functionality is only available from commands, and it doesn’t yet have coloring by attribute.  However, it does have rainbowing (e.g. different color for each residue in a chain or for each chain in a structure) and this does allow specifying your own colors like Chimera “rangecolor” or a nice new thing, fetching and using palettes from the Colourlovers web site.  Although the program isn’t available yet you can see this described in the ChimeraX color command documentation.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#cmap-options>

See also our most recent holiday card and the associated ChimeraX script (linked at the bottom of the page):
<http://preview.rbvi.ucsf.edu/Outreach/card-gallery/2015-ribosome/ribosome.html>

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 14, 2016, at 11:48 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi,
> Render by attribute currently only has five pre-defined palettes (Red-blue, blue-red, cyan-maroon, rainbow, and gray). Often I will use the same color palette repeatedly for the same task in Render by Attribute (e.g. dodger-blue/white/orange red for hydrophobicity). Is it possible to make such custom palettes persist in the drop down menu in Render by attribute? If not would it be possible to add such an option in ChimeraX?
> Cheers,
> Oli.




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