The commands in this section are primarily used for manipulating atoms. There is a wide range of commands and options.
Some commands require both sets of coordinates.
The syntax of the atom-selection is given in section Atom Selection . The syntax of the hbond-spec is given in section Syntax of the Hydrogen Bond Command . The other coordinate set is only changed by the SWAP command and the ORIEnt RMS command when the specified atoms are not centered about the origin. The selection specification should be at the end of the command. The default atom selection includes all atoms.