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.
Select A not B
- Select A and B
- Select A or B