Surfaces
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Molecular surfaces can be visualized.
Five color schemes are available for surfaces:
- Color by Charge Charged amino acids close to the surface will show as red (negative) or blue (positive) areas on the surface, with a color gradient that depends on the distance of the charged atom to the surface.
- Color by Element Smoothed out coloring based on the classic CPK coloring of the heteroatoms close to the surface.
- Color by Temperature Smoothed out coloring based on the b-factors for the atoms close to the surface. The b-factors are a measure of uncertainty or disorder in the atom position; the higher the number, the higher the disorder. The color scale goes from blue (0) over white (50) to red (100).
- Color by Entry Each surface is assigned its own specific color.
- Custom Color The user selects a surface color from a palette.
A surface spanning multiple molecules can be visualized by making a custom atom group that includes all atoms from the molecules (see Custom atom groups)