Selecting
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In many modules there are menu commands to select atoms:

* Select All: select all atoms in your system.

* Invert Selection: all atoms in your system currently not selected
  will be the new selection.

* Select Molecule: extent the current selection so that all atoms
  connected (by bonds as visible) to it are included in the selection.

* Select Connected: extent the current selection so that all atoms
  directly connected (by bonds as visible) to it are included in the
  selection. Thus repeated use of this command will select all atoms
  in your molecule (same as Select Molecule).

* Select Atom Close To Origin: select one atom close to the origin.
  Often useful to select one atom in a crystal, and next selecting
  atoms in a sphere around it (with the next command).

* Select Within Radius: set the selection to all atoms in a sphere
  with specified radius around the center of the current selection.

* Make Selection Cappable: extent the current selection such that it
  is acceptable as a region for the Hybrid engine, were all bonds to
  other parts will be capped. A cappable region should not have bonds
  with an order > 1.25 to atoms not in the region, and atoms outside
  the region should have at most one bond to atoms inside the region.
  This command will extent the selection so that these requirements
  are handled.

* Select Atoms Of Same Type / PDBName: extent the selection with atoms
  with the same Type (element) or PDBName.
