The atom selection feature in X-PLOR can be used to solvate a solute, such as protein or nucleic acid. Suppose the user has set up coordinates and molecular structure files for the solute (``solute.pdb" and ``solute.psf") and for a box of water (``water.pdb" and ``water.psf" with SEGId ``WAT") that is large enough to enclose the solute. The following X-PLOR script will create a composite coordinate and molecular structure file (``overlay.pdb" and ``overlay.psf") deleting all waters that penetrate the protein:
structure @solute.psf end
coordinates @solute.pdb
structure @water.psf end
coordinates @water.pdb
delete
selection=
( byres
( segid "WAT"
and ( ( not segid "WAT" and not ( hydrogen ) ) around 2.6 )
))
end
write structure output=overlay.psf end
write coordinates output=overlay.pdb end
If the box of water molecules is not large enough, it can be made
larger by duplicating and translating the original box (cf.
Section 3.10).