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Color categories

VMD maintains a database of the colors used for the molecules and the other graphical objects in the display window. The database consists of several color categories; each color category contains a list of names, and each name is assigned a color. For example, there is a Resname color category, and within this category there are many names; one for each of the available residue names. Some of these are ALA, CYS, and PRO. Each name can be assigned a color from a list of 33 available colors called the color map. The RGB value of each color can be modified directly in the Color window. To color items in a gradation manner, there are additional 1024 colors used in the color scale.

The different color categories in VMD are listed in table 6.2. The Color window can be used to change the assignment of colors to the names in each of these categories. For example, to change the color used to draw Arginine residues when molecules are colored by residue, you would use the Color window, select the `Resname' category, select the `Arg' name there, and then pick the color to use for Arginine's from the list of colors next to the names.


Table 6.2: Color categories used in VMD.
Category Contents
Display Color of background, gradient, depth cueing, text
Axes The components of the axes
Name The available atom names (color by Name)
Type The available atom types (color by Type)
Element Atomic elements (color by Element), with ''X'' for unknown
Resname The residue names (color by ResName)
Restype The residue types (color by ResType)
Chain The one-character chain identifier.
Segname The segment names (color by SegName)
Conformation The available conformation codes (color by Conformation)
Molecule The names assigned to each molecule (color by Molecule)
Highlight The protein, nucleic, and non-backbone colors
Structure The secondary structure type (helix, sheet, coil) (color by Structure)
Surface The surface types
Labels The different labels (atoms, bonds, etc.)
Stage The colors for the checkboard stage



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