Structure Browser shows the internal structure of the loaded data and is most useful for displaying protein and DNA structures. Each level of hierarchy is marked by different icon and corresponding naming of the items in the tree display. Chain labels contain a chain id, as it appears in the structure file. If no id is available, the chains are assigned the default symbol "_". Residue labels contain the residue name and its number. For DNA, single-letter notation is used, while for the proteins, residues are labeled with the three-letter amino acid code.

For small molecules, the browser works equally well, but usually shows one default chain and one residue. If a small molecule structure was built from fragments using Builder, each individual fragment is assigned to a separate residue.

Residues can be renamed (as well as atoms). However, it's not recommended for amino acids or DNA bases, since the type of the residue is derived from its name. If an ALA is changed to AAA, Sirius will no longer recognize it as an amino acid and will treat it as a ligand or unnatural amino acid. Therefore, residue renaming should be used with ligands and small molecules.

Also, atom renaming should be used carefully, since their names typically consist of the element symbol, followed by number. Use this feature only to correct errors in the data.

If an item is invisible in the 3D workspace, it's shown in light gray color. Typically, water molecules found in protein structures are invisible and belong to one chain (usually, the last one). Water molecules can be shown by using the option in Preferences.

The buttons at the lower subpanel provide access to dialogs to hide/show selected items (Display), render structure using the available representations (lines, stick, ball/stick and space-filling), and color the current selection. These choices are also available from the Action menu in the panel menubar. Any current selections can be removed by choosing Action -> Clear selection. Alternatively, clicking anywhere in the 3D workspace or in Sequence Viewer outside of the sequences will clear selection throughout the application.