Sirius features a command line interpreter that can be used to quickly manipulate structure appearance and orientation. The set of commands has been patterned after RasMol, so it’s fully compatible with existing scripts. Additional commands introduced in Sirius have been added to provide support for manipulation of multiple structures loaded at the same time, and to enable more flexible selection.
Existing RasMol scripts can be imported and run within Sirius to produce high quality representations of encoded molecular scenes. Since RasMol uses a coordinate system that differs from that Sirius, internal conversion is performed when RasMol scripts are imported, so that any orientation changes are shown correctly. Any manually entered commands, however, are executed according to the Sirius coordinate system. For details, refer to Sirius help.
Sirius supports a number of predefined atom/residue sets and color schemes, as well as allows for editing of scripts using the Command Panel interface. In addition, logical operators and parentheses can be used to create complex selection commands.