Manipulate Tool

The manipulate tool allows you to move individual atoms or selected fragments in space.

Left click and drag: Translate atoms or fragments in space.
Middle click: Push atoms or fragments through space (up and down relative to the screen).
Right click and drag: Rotate atoms or fragments in space (only does something when at least one atom is selected).

If a set of atoms is selected, then the entire set will be manipulated together. This is an effective way to move fragments into position.