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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.
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Justin Gullingsrud
Tue Apr 6 09:22:39 CDT 1999