The Structure items are not selectable and can be expanded and collapsed by clicking the triangular icon or double-clicking the title. The rest of the objects can be selected by mouse clicking. Once a part of the tree is selected, the view is updated in the 3D workspace and in the sequence viewer.

Multiple selection can be made by holding down Control key. A residue is considered selected and highlighted if all of its atoms are selected. The same applies to chains. For contiguous selections of residues, it is recommended to use the sequence viewer, which supports this feature.

Once a part of the tree is selected, you can use the buttons in the lower panel to color, render or show/hide parts of the display. These functions are also provided through the menu items in the Action menu. It also contains Clear selection option, which removes current selection from the tree and deselects the corresponding parts of the display in 3D workspace and sequence viewer.

Right-clicking on a tree item displays a shortcut menu with item-specifc options. All components of the tree have the option to show their information, which brings up the Information Viewer panel in the lower part of the Structure Browser. Information Viewer can be cleared and hidden/shown from the menu items in the View menu. Also, its content can be printed.

Individual atoms can be brought into focus by selecting Focus view on atom. This option centers the view on the selected atom and moves it close to the viewer. This option is useful for selecting out the atoms of interest in large complex structures where locating them in the 3D window may be difficult.

Residues and atoms can be renamed. All items can be colored and rendered. Chains also have this option, which applies to their atomic structure (not ribbon cartoons).

Ribbons can be shown or removed via the same shortcut menu if a chain is right-clicked. To add a ribbon, a small dialog window is displayed that asks the user to select type of the ribbon cartoon, as well as the quality level. By default, a low quality ribbon with regular helices is shown. A higher quality can be set by dragging the slider in the quality setting panel.

It is recommended to use high quality ribbon settings only for exporting images, since they slow down selection, rendering and coloring of the structure.