Coloring Methods

As described in chapter 5, each representation for a molecule has a specific coloring method. The coloring method determines how the color for each atom in the representation (view) is determined. These different methods use the colors assigned to the names in the categories listed above, and use those names to color the atoms. Molecular drawing methods which also draw the bonds between atoms will always color each half of the bond separately, using the color of the nearest atom for each half. Table 5.3 lists the different coloring methods available. The description for each method explains the source of the information used to determine the color.

Table 5.3: Molecular coloring methods.

Method	Description
Name	Atom name, using the Name category
Type	Atom type, using the Type category
ResName	Residue name, using the Resname category
ResType	Residue type, using the Restype category
ResID	Residue identifier, using the resid mod 16 for the color
Chain	The one-character chain identifier, using the Chain category
SegName	Segment name, using the Segname category
Molecule	Molecule all one color, using the Molecule category
Structure	Helix, sheet, and coils are colored differently
ColorID	Use a user-specified color index (from 0 to 15)
Beta	Color scale based on beta value of the PDB file
Occupancy	Color scale based on the occupancy field of the PDB file
Mass	Color scale based on the atomic mass
Charge	Color scale based on the atomic charge
Pos	Color scale based on the distance of each atom to the
	center of the molecule. This is an interesting way to
	view globular systems.
User	Provides a single data value for each atom for each timestep
Index	Color scale is based on the atom index. Due to the way
	the PDB file is organized, this actually looks nice.
Backbone	Backbone atoms green, everything else is blue
Throb	Animates colors through the active color scale based on wall clock time
Timestep	Color scale based on the current trajectory timestep frame