load 1DSZ.pdb

define ribose_polar dna and *.O?*
define ribose_nonpolar dna and *.C?*
define phosphate_polar dna and *.O?P
define phosphate_nonpolar dna and *.P
define n_base_large_polar (DA.N6, DA.N7) or (DG.O6, DG.N7) or (DC.N4) or (DT.O4)
define n_base_large_nonpolar (DA.C6, DA.C5, DA.C5) or (DG.C6, DG.C5, DG.C8) or (DC.C6, DC.C5, DC.C4) or (DT.C6, DT.C5, DT.C4, DT.C7)
define n_base_small_polar (DA.N3, DA.N9) or (DG.N2, DG.N3, DG.N9) or (DC.O2, DC.N1) or (DT.O2, DT.N1)
define n_base_small_nonpolar (DA.C2, DA.C4) or (DG.C2, DG.C4) or (DC.C2) or (DT.C2, DT.C6)

restrict none
select dna
backbone
wireframe
zoom 300
pause

select ribose_polar
cpk 50
select within (3.5, ribose_polar) and (*.O?? or *.N??) and protein and *:A
cpk 100
pause

cpk off
select ribose_polar
cpk off
select ribose_nonpolar
cpk 50
select within (4.5, ribose_nonpolar) and (*.C?? or *.P?? or *.S??) and protein and *:A
cpk 100
pause


cpk off
select ribose_nonpolar
cpk off
select phosphate_polar
cpk 50
select within (3.5, phosphate_polar) and (*.O?? or *.N??) and protein and *.A
cpk 100
pause

cpk off
select phosphate_polar
cpk off
select phosphate_nonpolar
cpk 50
select within (4.5, phosphate_nonpolar) and (*.C?? or *.P?? or *.S??) and protein and *:A
cpk 100
pause


cpk off
select phosphate_nonpolar
cpk off
select n_base_large_polar
cpk 50
select within (3.5, n_base_large_polar) and (*.O?? or *.N??) and protein and *:A
cpk 100
pause

cpk off
select n_base_large_polar
cpk off
select n_base_large_nonpolar
cpk 50
select within (4.5, n_base_large_nonpolar) and (*.C?? or *.P?? or *.S??) and protein and *:A
cpk 100
pause


cpk off
select n_base_large_nonpolar
cpk off
select n_base_small_polar
cpk 50
select within (3.5, n_base_small_polar) and (*.O?? or *.N??) and protein and *:A
cpk 100
pause

cpk off
select n_base_small_polar
cpk off
select n_base_small_nonpolar
cpk 50
select within (4.5, n_base_small_nonpolar) and (*.C?? or *.P?? or *.S??) and protein and *:A
cpk 100
pause