Palettes
A palette is an ordered set of colors or value,color pairs
specified with the palette option
of color,
coulombic,
mlp,
or measure convexity.
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 Key,
Surface Color,
key,
color list,
color specification,
color schemes
The following palettes are predefined in ChimeraX:
[back to top: Palettes]
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) |
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Set3-12 (3-12) |
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Pastel1-9 (3-9) |
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Set1-9 (3-9) |
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Pastel2-8 (3-8) |
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Set2-8 (3-8) |
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Dark2-8 (3-8) |
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Accent-8 (3-8) |
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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) |
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OrRd-5 (3-9) |
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Oranges-5 (3-9) |
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YlOrBr-5 (3-9) |
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Greens-5 (3-9) |
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BuGn-5 (3-9) |
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YlGn-5 (3-9) |
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PuBuGn-5 (3-9) |
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PuBu-5 (3-9) |
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GnBu-5 (3-9) |
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Blues-5 (3-9) |
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YlGnBu-5 (3-9) |
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Purples-5 (3-9) |
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RdPu-5 (3-9) |
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BuPu-5 (3-9) |
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PuRd-5 (3-9) |
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YlOrRd-5 (3-9) |
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Reds-5 (3-9) |
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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) |
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PiYG-5 (3-11) |
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PRGn-5 (3-11) |
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BrBG-5 (3-11) |
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RdBu-5 (3-11) |
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PuOr-5 (3-11)* |
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RdYlGn-5 (3-11) |
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Spectral-5 (3-11) |
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RdYlBu-5 (3-11) |
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*The “PuOr” name seems backwards, but that's the way it is.
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UCSF Resource for Biocomputing, Visualization, and Informatics /
November 2022