#pymol 
pymol align.pml

cat 1SX4_nuc_A.pdb 1SX4_nuc_B.pdb 1SX4_nuc_C.pdb 1SX4_nuc_D.pdb 1SX4_nuc_E.pdb 1SX4_nuc_F.pdb 1SX4_nuc_G.pdb > ADP_cis-ring.pdb

touch addTo
echo "TER" > ter.pdb
files=`ls ATP_?.pdb`
for i in H I J K L M N 
do
	grep "HETATM" ATP_${i}.pdb > tmp.pdb
	cat addTo tmp.pdb ter.pdb MG_${i}.pdb > tmp
	mv tmp addTo
done	
sed -i 's/END/TER/g' addTo
mv addTo ATP_trans-ring.pdb

#cat ATP_H.pdb MG_H.pdb ATP_I.pdb MG_H.pdb ATP_J.pdb MG_H.pdb ATP_K.pdb MG_H.pdb ATP_L.pdb MG_H.pdb ATP_M.pdb MG_H.pdb ATP_N.pdb > ATP_trans-ring.pdb