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Palettes

A palette is an ordered set of colors or value,color pairs used for coloring sequentially or by value with the palette option of color or mlp. The colors can be specified individually, or the name of a palette can be given. Named palettes consist of colors only. The command palette list lists the names of the available palettes in the Log. See also: color list, color specification, initial colors

The following palettes are predefined in ChimeraX:

ColorBrewer Palettes

Users should cite: www.ColorBrewer.org, color specifications and designs by Cynthia A. Brewer, Pennsylvania State University.

ColorBrewer palette names are predefined in ChimeraX and summarized in the tables below. Only a selected number-version is shown for each name, with the range of available numbers given in parentheses. Capitalization of the name is not important. All versions can be previewed (albeit without their names) and assessed by other criteria such as suitability for colorblind viewers at the ColorBrewer website.

Palettes for qualitative data, default 6 colors (a qualitative N-color palette uses only
the first N colors shown, from left to right):
Name Colors
Paired-12 (3-12)
Set3-12 (3-12)
Pastel1-9 (3-9)
Set1-9 (3-9)
Pastel2-8 (3-8)
Set2-8 (3-8)
Dark2-8 (3-8)
Accent-8 (3-8)

Palettes for sequential data, default 5 colors (colors in the name are interpolated across the range and from light to dark; the more colors used, the darker the last color):
Name Colors
Greys-5 (3-9)
OrRd-5 (3-9)
Oranges-5 (3-9)
YlOrBr-5 (3-9)
Greens-5 (3-9)
BuGn-5 (3-9)
YlGn-5 (3-9)
PuBuGn-5 (3-9)
PuBu-5 (3-9)
GnBu-5 (3-9)
Blues-5 (3-9)
YlGnBu-5 (3-9)
Purples-5 (3-9)
RdPu-5 (3-9)
BuPu-5 (3-9)
PuRd-5 (3-9)
YlOrRd-5 (3-9)
Reds-5 (3-9)
Palettes for diverging data, default 5 colors (colors are interpolated across the range with a light color in the middle; the more colors used, the darker the ends):
Name Colors
RdGy-5 (3-11)
PiYG-5 (3-11)
PRGn-5 (3-11)
BrBG-5 (3-11)
RdBu-5 (3-11)
PuOr-5 (3-11)*
RdYlGn-5 (3-11)
Spectral-5 (3-11)
RdYlBu-5 (3-11)
*The “PuOr” name seems backwards, but that's the way it is.

UCSF Resource for Biocomputing, Visualization, and Informatics / September 2017