load ==1BDT.pdb
background white
select all
wireframe 40
cartoons off
color cpk
select not dna
color gray
color translucent
select water 
color translucent 1.0
select all
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 green
cpk
select within (3.5, set2) and polar_protein
color translucent 0.0
color pink
cpk
select within (3.5, plg) and polar_protein
color translucent 0.0
color yellow
cpk

pause
 
select protein
color translucent
cpk off
color gray
select within (4.5, set1') and protein_nonpolar
color translucent 0.0
color darkviolet
cpk
select within (4.5, set2') and protein_nonpolar
color translucent 0.0
color lightgreen
cpk
select within (4.5, nlg) and protein_nonpolar
color translucent 0.0
color lightblue
cpk
select within (4.5, nsg) and protein_nonpolar
color translucent 0.0
color brown
cpk