3.1.4 Atom Selection

    This very useful submenu allows you to selectively display portions of a molecule based on relationships to the picked atom. Presently this is the only way to define atom selections in a graphical fashion. All other selections must be described via a text-based entry form. The following criteria may be used. In each case, VMD will render only those atoms which have the following property in common with the selected atom

• Same Residue
• Same Chain
• Same Segname
• Same Fragment

In addition, the currently selected atom can be used as a representative of the entire molecule by choosing to render only the following atoms of the molecule.

• backbone - VMD should display backbone atoms only
• protein - only atoms comprising a protein should be displayed
• nucleic - only display atoms comprising nucleic acids
• water - only display water atoms in the molecule
• not waters - only display non-water atoms in the molecule
• heavy atoms- only display the heavy atoms of the molecule

  Note that this submenu only affects the first representation (view) listed in the Graphics form for the given molecule.