JMV implements a variety of ways to color the molecule. To change the coloring method, select ``Color by'' from the ``View menu'', and select one of the choices. The choices are:
| Style | Description |
| Name | Each atom type is assigned a different color. These colors are:
Carbon: Cyan
|
| Index | The pdb file assigns each atom a unique index identifier. In the Index color scheme, JMV creates a color gradient that creates a smooth color transition going through each atom, in order of their index numbers. |
| Resname | In the pdb file, each atom belongs to a certain residue.The Resname color scheme assigns a color to each Residue Name (based on the gradient), and colors each residue with the given color. |
| Chain | In the pdb file, each atom belongs to a certain Chain. The Chain color scheme assigns a color to each Chain (based on the gradient), and colors each chain with the given color. |
| Segment | In the pdb file, each atom belongs to a certain Segment. The Segment color scheme assigns a color to each Segment (based on the gradient), and colors each segment with the given color. |
| Structure | Certain series of atoms may have a ``structure'' associated with them. If these structures are written n the pdb file, JMV can color the molecule by structure. The structures and their colors are:
No structure specified: White Helix: Red Turn: Green Sheet: Blue |