This example was developed in 1999 and the text below reflects that. Recent versions of Chimera include the Render by Attribute tool, which is for the most part more useful than the ResProp tool described below.
Another recently-developed tool allows the coloring of amino-acid residues by residue property (such as hydrophobicity). The above right panel has a menu of residue property schemas (which can be added to by the user) and shows which residues are selected in that schema. The colors which are assigned to selected and unselected main/side chains in the schema is shown to the right side of the panel. These colors can be changed at will. The color editor used to change colors is shown in the lower right of the image. Note that a color can have a transparency component. In the image a flavin bound to flavodoxin is shown. The surface associated with main chain atoms has been given a significant transparency component, which allows some deep binding-pocket interactions to be viewed.
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