Molecular Drawing Methods

Each molecule in VMD is drawn as a collection of several representations, of the molecule. A representation is just one particular way of drawing the molecule, and consists of several characteristics:

• An atom selection, which determines which of the atoms in the molecule will be included in the view. This selection is entered in the text input field at the bottom of the Graphics window. Atom selections don't apply when drawing volumetric data such as an electron density map, electrostatic potential map, etc. Section 6.3 describes the syntax used to select atoms.

• A drawing method (representation style), which determines what shape to draw the atoms, bonds, and other components of the molecule. Section 6.1 describes the rendering methods available in VMD.

• A coloring method, which determines how to color each of the atoms and bonds included in the view. The Graphics window contains controls to set the coloring method at the right of the window. Section 6.2 describes VMD's coloring methods.

• A material, which determines the shininess, opacity, and other lighting and shading characteristics used when rendering the molecule.

A molecule can contain any number of different representations, and complex pictures of the molecule can be generated by creating views with different selections, coloring schemes, and rendering methods. For example, the protein backbone can be drawn as a smooth tube in one view, and important residues in the protein can be drawn as spheres or licorice bonds in other views. When a molecule is first loaded, it is given a `default' view, which will draw all the atoms as lines and points, coloring each atom by what kind of element it is.