Selecting can be done via atom expressions or based on geometry. The selection expressions used in Jmol can be used for the "select" and the "display within" commands.
Combining selection statements
The combination of selection statements in Jmol is based on Boolean logic, using the statements And, Or, and Not, in a slightly different way than these are used in conversational language.
Example: We have a system consisting of water and a peptide chain. We are interested in selecting oxygen atoms. Let's call the set of atoms in the peptide chain A, and all oxygen atoms B.
Selects all atoms in the peptide chain.
Select A or B
Selects all atoms in the peptide chain, and all oxygen atoms, including the oxygen atoms in the water molecules.
Select A and B
Selects only the atoms that are both belonging to the peptide chain, and oxygen atoms. Therefore it selects only the oxygen atoms in the chain.
Select A not B
Selects the atoms in the peptide chain, but not the ones that are oxygen atoms.
Select (A or B ) and (not (A and B))
Selects all the peptide chain atoms and all the oxygen atoms, but not the oxygen atoms in the peptide chain.