Molecular Drawing Methods

Each molecule in VMD is drawn as several representations, or views, of the molecule. A view is just one particular way of drawing the molecule, and consists of three characteristics:

• A rendering method (representation style), which determines what shape to draw the atoms, bonds, and other components of the molecule. This chapter describes the different 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 form contains controls to set the coloring method at the right of the form. Chapter §  describes the different coloring methods.

• 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 form. Chapter §  describes the syntax used to select atoms.

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.

All of the different rendering methods have various parameters which determine how they are drawn. For each method, there are controls in the Graphics form which modify the associated parameters, such as the line width and sphere resolution (the graphical controls are described in section §). Table 5.1 lists the available rendering methods, and the following sections describe these methods and the parameters which modify their appearance.

Table 5.1: Molecular view representation styles.

Representation styles	Description
Lines	simple lines for bonds, points for atoms
Bonds	lighted cylinders for bonds
CPK	scaled VDW spheres, with cylinders for bonds
Points	just points for atoms, no bonds
VDW	solid van der Waal spheres for atoms, no bonds
Dotted	dotted van der Wall spheres for atoms, no bonds
Solvent	dotted representation of the solvent accessible surface
Trace	connected cylindrical segments through C${}_\alpha$ atoms
Licorice	spheres for atoms, cylinders for bonds, same radius
Ribbons	flat ribbon through the C${}_\alpha$ atoms
Tube	smooth cylindrical tube through the C${}_\alpha$ atoms
Cartoon	cartoon diagram (cylinders and ribbons) based on secondary structure
MSMS	molecular surface as determined by the program MSMS
HBonds	display hydrogen bonds
Surf	molecular surface as determined by SURF
Off	do not draw anything