This is useful when two residues of separate layers are exactly superposed, because only the residue of the current layer will be selected. No confusion is possible. Acid This will select Asp and Glu. Basic This will select Arg Lys and His. Pro Trp and Val Helices, Strands, Colis Select all the corresponding secondary structure elements.
Visible Groups Select the residues currently visible.
It does take into account the slab mode, and will not only select groups that have a show mark in the Control Panel. Reconstructed aa Select residues whose sidechain has been reconstructed. Remember that incomplete pdb files are completed upon loading. Usually, reconstructed sidechains lay at the surface and are highly mobile. This will let you extend a selection aroud a previously selection.