A while back I asked if anyone knew how waters could be moved
automatically to the closest symmetry site in retrospect to the "main"
structure. Several people asked me to give a brief summary of the
results. I may have missed listing some of them, but I am thankful to
all who replied.
1) NDB does this automatically upon submission
2) CCP4
3) CNS appears to have the capability to do this (see shift_solvent.inp)
4) You can do it with O. Just write all the solvent molecules into a
separate .pdb. Alternatively, there is the Swiss PDB Viewer, available
at http://www.tigem.it/TIGEM/HTML/Swiss-PdbViewer%20Home%20Page.html
5) Shelx