$tntbin/overlay << $eof INCLUDE core5r.cor SELECT C1A NA C4A CHB C1B C2B C3B CAB C4B NB SELECT CHC C1C NC C4C CHD C1D C2D C3D CAD C4D ND CHA TARGET 360 OVERLAY 362 APPLY 362 OVERLAY 364 APPLY 364 OVERLAY 366 APPLY 366 OVERLAY 368 APPLY 368 OVERLAY 370 APPLY 370 OVERLAY 372 APPLY 372 PUNCH output.cor ATOMC $eof if ($status >< 0) then exit 1
This example is more complicated. Here Overlay reads in the coordinates of the bacteriochlorophyll core of the bacteriochlorophyll-a containing protein, selects for consideration only the atoms in the conjugated ring system, superimposes each ring, in turn, onto ring 360, and writes the resulting coordinates to the file output.cor.