There are now two new attributes in Atom to assist in working with alternate locations: Atom.allLocations returns a list of atoms sharing the atom's location, from highest occupancy to lowest. In the most common case (no alternate locations) it is a list with one element, the current atom. Atom.primaryBonds is similar to Atom.bonds, but holds at most one bond to a location. If this atom has an alternate location indicator, then primaryBonds will hold bonds to atoms with the same indicator, or no indicator. If this atom has no indicator, primaryBonds will hold bonds to the highest-occupancy atoms of bonded locations. --Eric