The SELECT command

This command, preceding a modifier, will tell the modifier what to act on.  There are scores of ways to tell this command what to select - here is a whole page about it.

I dug through much of that document and distilled out what I believed to be some of the most handy expressions and put them on this page

Modifying commands

There is a whole subset of commands that can follow a "select" and DO something to the selected molecules.  The most common uses are modifying the color of the selected atoms, or changing the method used to draw those atoms (from the standard wirefram model to a space-filling model for example) Commands and examples can be seen here.