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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
SegName Segment name, using the Segname category
Molecule Molecule all one color, using the Molecule category
Structure Helix, sheet, and coils are colored differently
Chain The one-character chain identifier, using the Chain category
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.
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



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