Specifying Atomic Sets

For many commands in define you will have to specify a set of atoms on which that command shall act. There are three ways to do that:

• You may enter all or none, the meaning of which should be clear (entering none makes not much sense in most cases, however).
• You may specify a list of atomic indices like 1 or 3,5,6 or 2,4-6,7,8-10 or similar.
• You may also enter atomic identifiers which means strings of at most eight characters: the first two contain the element symbol and the remaining six could be used to distinguish different atoms of the same type. For example, if you have several carbon atoms in your molecule, you could label some c ring and others c chain to distinguish them. Whenever you want to enter an atomic identifier, you have to put it in double quotation marks: "c ring".

You should take into account that define also creates, from the atoms you entered, all others according to symmetry. If necessary, you will therefore have to lower the (formal) symmetry before executing a command.