Sirius has a full-featured command line interface that allows for fast access to most of the visualization features of the application. This interface is intended as a shortcut, so any command line operation can be reproduced using the menu-driven interface. A set of commands can be run in sequence or saved to a script file.

The command syntax was patterned after RasMol, in order to make the transition easier for the RasMol users. Most of the predefined sets (aminoacids, ligand, solvent, etc.) have been included in the syntax, as well as the commonly used color schemes. The command line interpreter also supports combined logical expressions that define atom sets, including those with AND, NOT and OR operators. At this time, Sirius interpreter does not support nested parantheses. However, more complex atoms sets can be defined in more than one command, using the addselect command that adds selection to an already existing selection without replacing it.

Sirius features several additional commands that are relevant in the Sirius environment and provide control over some advanced aspects of the application (for example, the connect command that causes all following commands to be applied to the named structure). For complete list of supported commands, refer to the table under Command line interface. Import of existing RasMol scripts is described in the second section.