Table 2 Subpanels of the retractable right-side control panel.

Selection

The left-side subpanel allows selection of any model, chain, residue, water, heterogen, or atom of the protein. This subpanel is always present, whereas the right-side subpanel can be changed to any of the subpanels listed below.

Decorations

Applies texture maps and other special effects to ribbon and tube segments (the term segment refers to the length of a tube or ribbon that corresponds to an individual amino acid). This subpanel is visible in Figure 1.

Cartoon Color

Sets the color of tube and ribbon segments. Default colors based on region or amino acid type can be used, or a color chooser dialog box can be opened.

Cartoon Visibility

Sets any segment or group of segments in a tube or ribbon to be opaque, translucent, or invisible.

Cartoon Side Chains

Used to display amino acid side chains in combination with tubes or ribbons. The side chains can be shown as space filling, balls and sticks, or sticks.

Motion

Allows constant motion about the x-axis and/or y-axis of the protein. The frames per second will be displayed in the upper left of the canvas.

Antialiasing

Provides options for smoothing out the aliasing (jagged diagonal line) effect that often occurs at the edges of geometrically defined objects.

Atom Color

Sets the color of atoms in a space filling, balls and sticks, or sticks style display. Default colors based on atom or amino acid type can be applied, or a color chooser dialog box can be opened.

Atom Visibility

Sets any atom or group of atoms to be opaque, translucent, or invisible. A slider allows any degree of translucency from 0 to 100%.

Atom Scale

Adjusts the radii of spheres in a space filling or balls and sticks style display.

Tiling

Can be used to turn off automatic tiling (level of detail control) for spheres and cylinders. This panel has no effect on ribbon and tube style displays.