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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, 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 located
here). 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 rendering methods.
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Andrew Dalke
Tue May 14 16:49:45 CDT 1996