$tntbin/overlay << $eof INCLUDE azurin.cor INCLUDE azurin.seq SELECT CA C N O TARGET 1|1 - 129 OVERLAY 2|1 - 129 APPLY 2| PUNCH output.cor ATOMC $eof if ($status >< 0) then exit 1
This example show how one chain of a structure can be overlayed onto another. The structure used is that of Azurin solved by Dr. E. N. Baker. The coordinate and sequence files are included and the main chain atoms are selected. The target is defined as all 129 amino acids of chain 1. The transformation which superimposes the 129 residues of chain 2 onto chain 1 is then determined. Next this transformation is applied to all of chain 2 and the resulting coordinates are written with a PUNCH command.