load ==1TRO.pdb
select all
cartoons off
wireframe 50
color cpk
select not dna
color white
color translucent
select water 
color translucent 2.0
select dna
cpk off
select dna
wireframe 50
define set1 (*.O?* and dna)
define set1'(*.C?* and dna)
define polar_protein (oxygen or nitrogen) and protein 
define set2 (*.OP? and dna)
define set2' (*.P and dna)
define plg (DA.N6, DA.N7) or (DG.O6, DG.N7) or (DC.N4) or (DT.O4)
define psg (DA.N3, DA.N9) or (DG.N2, DG.N3, DG.N9) or (DC.O2, DC.N1) or (DT.O2, DT.N1)
define protein_nonpolar (carbon or sulfur) and protein
define nlg (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 nsg (DA.C2, DA.C4) or (DG.C2, DG.C4) or (DC.C2) or (DT.C2, DT.C6)
select within (3.5, set1) and polar_protein
color translucent 0.0
color orange
cpk 250
select within (3.5, set2) and polar_protein
color translucent 0.0
color lightgreen
cpk 250
select within (3.5, plg) and polar_protein
color translucent 0.0
color green
cpk 250
select within (3.5, psg) and polar_protein
color translucent 0.0
color yellow
cpk 250 
pause
 
select protein
color white
color translucent
cpk off

select within (4.5, set1') and protein_nonpolar
color translucent 0.0
color lightblue
cpk
select within (4.5, set2') and protein_nonpolar
color translucent 0.0
color blue
cpk
select within (4.5, nlg) and protein_nonpolar
color translucent 0.0
color violet
cpk
select within (4.5, nsg) and protein_nonpolar
color translucent 0.0
color magenta
cpk