The question: "Is there an efficient way to keep track of alternate conformations in O ?"
Alwyn replied: "There should be no problem seeing them in O but in 5.9 there would be problems using Tor_res, for example. If the coords are read into O as XPL files, the 1st char of the segid gets added to the residue name. This could then give residues with just some atoms e.g. just side chains. The new Tor_general command in O 5.10 will allow you to change them."