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Beneath that Display section is the Color section which contains eight different coloring buttons arranged as two rows of four buttons. In the first row of buttons, the first button prompts for a specific single color which is applied to the surface. The second button colors the surface using the color of the atom associated with the individual surface vertices. This atom is typically the nearest atom to the vertex from the molecule that generated the surface. The third button colors the surface by concavity, where the most concave sections of the surface are colored red and the rest are colored white. The fourth button in this row colors the surface by curvature, with green corresponding to the greatest amount of curvature and grey being the least. Examples of these color schemes can be seen in Figure 5.17.
[Color by Atom]
[Color by Concavity]
[Color by Curvature]
[Color by Electrostatics]
[Color by Distance]
[Color by Hydrogen Bond Potential]
[Color by Hydrophobicity]
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In the second row of buttons, the first button colors the surface by the electrostatic potential of the molecule that created the surface. The second button colors the surface by the distance from either the selected set of atoms or the visible set of atoms (if none are selected). Each band of color represents a distance of one angstrom from the selected set. The color banding is continuously repeated as the distance increases, but the colors fade to white with each repetition to show the distance effect. The third button colors the surface by the hydrogen bond potential of the molecule that created the surface. Donor regions are colored blue and acceptor regions are colored red. The fourth button colors the surface by hydrophobicity characterized by its electrostatic potential. Areas with high negative potential are colored red, areas with high positive potential are colored blue, while areas with very low electrostatic potential are colored yellow, and the rest are colored magenta.
If there is a set of vertices selected on a surface when one of the above coloring buttons is clicked, the coloring scheme will be applied only to those selected vertices as opposed to the surface as a whole.
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