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:

• rainbow (default for color command sequential coloring)
• red-white-blue or redblue (default for color command map coloring)
• blue-white-red or bluered
• cyan-white-maroon or cyanmaroon
• cyan-gray-maroon
• grayscale or gray
• lipophilicity (default for the mlp command, along with range -20,20)
• alphafold

  0

  50

  70

  90

  100

  (used to show the pLDDT confidence measure in the B-factor field of AlphaFold predictions)
• esmfold

  0.0

  0.5

  0.7

  0.9

  1.0

  (used to show the pLDDT confidence measure in the B-factor field of ESMFold predictions)
• pae

  0

  5

  10

  15

  20

  25

  30

  (the default for plotting PAE from AlphaFold or from ESMFold)
• paegreen

  0

  5

  10

  15

  20

  25

  30

• paecontacts

  0

  5

  10

  15

  20

  (the default for alphafold contacts)
• ColorBrewer palettes

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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.