PyMOL is governed by a series of concepts that you should eventually become quite familiar with if you are to get the most out of the program.

Unique Names | Objects | Name Patterns | Selection Expressions

Frame | State

Atom | Bond | Residue | Chain | Segment

Fragment | Molecule | Molecular Object

Coordinate Set

Alternate Locations (as identified in PDB files)

Selections

Representations

Command | Method

Internal GUI | External GUI | External GUI Skin