11.07.2015 Views

VMD User's Guide

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Chapter 5Molecular Drawing MethodsEach molecule in <strong>VMD</strong> is drawn as a collection of several representations, of the molecule. A representationis 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 inthe view. This selection is entered in the text input field at the bottom of the Graphics form.Atom selections don’t apply when drawing volumetric data such as an electron density map,electrostatic potential map, etc. Section 5.3 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 5.1 describes the rendering methodsavailable in <strong>VMD</strong>.• A coloring method, which determines how to color each of the atoms and bonds included inthe view. The Graphics form contains controls to set the coloring method at the right of theform. Section 5.2 describes <strong>VMD</strong>’s coloring methods.• A material, which determines the shininess, opacity, and other lighting and shading characteristicsused when rendering the molecule.A molecule can contain any number of different representations, and complex pictures of themolecule can be generated by creating views with different selections, coloring schemes, and renderingmethods. 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 linesand points, coloring each atom by what kind of element it is.5.1 Rendering methodsAll of the different rendering methods have various parameters which determine how they aredrawn. For each method, there are controls in the Graphics form which modify the associatedparameters, such as the line width and sphere resolution (the graphical controls are described insection 4.4.7). Table 5.1 lists the available rendering methods, and the following sections describethese methods and the parameters which modify their appearance.57

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