B4: How to change the color.
There are two ways to change the color of the displayed atoms, via the "Color", or by the "Change Color To" command. The first option will color the molecule with a number of useful coloring schemes (described below). The second option can be used to select a number of different colors. When the color change is combined with atom selection it is a powerful way to highlight certain areas of the molecule (i.e. active site residues).
Color Options (Select using Color from Main Menu):
In addition to the above predefined colors, you can also select from a list of colors using the "Change Color To" command. As an example, to change the molecule (or selected part of the molecule) to purple follow this series of menu selections: Select¬Change Color To¬Purple. The menus should look as shown to the left.
- CPK Colors:
Nitrogen (light blue)
Carbon (light grey)
- Amino Acid: Color coded by amino acid type.
- Shapely: Similar to Amino Acid.
- Group: Colors according to residue number, nice way to follow chain trace (from blue at the N-terminus to red at the C-terminus).
- Chain: Each chain (i.e. protein, DNA) is colored differently.
- Temperature: Colored according to temperature factor (from blue for rigid structures to red for mobile structures).
- Structure: Colored by secondary structure.
blue: reverse turns
white: everything else, i.e. unspecified