“clip” alters the positions of the clipping planes.
clip mode, distance [, selection [, state ]]
mode = near, far, move, slab, or atoms
distance is a floating point value
selection = atom selection (for mode=atoms only)
clip near, -5 # moves near plane away from you by 5 A
clip far, 10 # moves far plane towards you by 10 A
clip move, -5 # moves the slab away from you by 5 A
clip slab, 20 # sets slab thickness to 20 A
clip slab, 10, resi 11 # clip 10 A slab about residue 11
clip atoms, 5, pept # clip atoms in "pept" with a 5 A buffer
# about their current camera positions