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Coloring Methods

As described in chapter 6, 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 6.3 lists the different coloring methods available. The description for each method explains the source of the information used to determine the color.


Table 6.3: Molecular coloring methods.
Method Description
Name Atom name, using the Name category
Type Atom type, using the Type category
Element Atomic element, using the Element 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
Conformation Conformation, e.g. PDB alternate location identifier
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 radial distance from the molecule center
PosX, PosY, PosZ Color scale based on axial distance from the molecule center
User, User2, User3, User4 Color scale assigned by per-atom values for each timestep
PhysicalTime, Timestep Color scale based on the physical (simulation) time or
  timestep index associated with the displayed trajectory frame
Velocity Color scale based on the per-atom velocity value
  associated with the displayed trajectory frame
Fragment Color scale based on the VMD fragment index
Index Color scale based on the VMD atom index
Backbone Backbone atoms green, everything else is blue
Throb Color scale animated by the current wall clock time
Volume Surfaces are colored by the linked volumetric data set



next up previous contents index
Next: Coloring by color categories Up: Coloring Methods Previous: Color categories   Contents   Index
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