select all
restrict none
define ch ((*:B or *:C or *:D) and not AMP)
define o_in_rib ((*.O?* or *.O4' or *.O5') and ch)
define o_in_p ((*.O?P or *.OP?) and ch)
define c_in_rib ((*.C?* or *.C?') and ch)
define p_in_p (*.P and ch)
define n_in_dna (*.N? and ch)
define nonpolprot (protein and (*.C?? or *.S?))
define polprot (protein and (*.O?? or *.N??))
define pol_bigdna (ch and (*.N4 or *.O4 or *.N6 or *.O6 or *.N7))
define pol_smalldna (ch and (*.N2 or *.O2 or *.N3))
define nonpol_bigdna (ch and ((pyrimidine and (*.C4 or *.C5 or *.C6 or *.C7)) or (purine and (*.C5 or *.C6 or *.C8))))
define nonpol_smalldna (ch and ((pyrimidine and *.C2) or (purine and (*.C2 or *.C4))))

restrict none
select all
wireframe 50
pause
restrict ch
pause
select o_in_rib
cpk 200
echo Big red balls are oxygen atoms locared in ribose
pause
cpk off
select o_in_p
cpk 200
echo Big red balls are oxygen atoms located in phosphates
pause
cpk off
select n_in_dna
cpk 200
echo Big blue balls are nitrogen atoms located in nucleic bases
pause
cpk off
select polprot and within(3.5, o_in_rib)
cpk 200
echo Big balls are protein atoms creating polar interactions with oxygen atoms in ribose
pause
cpk off
select nonpolprot and within(4.5, c_in_rib)
cpk 200
echo Big balls are protein atoms creating hydrophobic interactions with carbon atoms in ribose
pause
cpk off
select polprot and within(3.5, o_in_p)
cpk 200
echo Big balls are protein atoms creating polar interactions with oxygen atoms in phosphates
pause
cpk off
select nonpolprot and within(4.5, p_in_p)
cpk 200
echo Big balls are protein atoms creating hydrophobic interactions with phosphorus atoms in phosphates
pause
cpk off
select polprot and within(3.5, pol_bigdna)
cpk 200
echo Big balls are protein atoms creating polar interactions with nucleic bases in big furrow
pause
cpk off
select nonpolprot and within(4.5, nonpol_bigdna)
cpk 200
echo Big balls are protein atoms creating hydrophobic interactions with nucleic bases in big furrow
pause
cpk off
select polprot and within(3.5, pol_smalldna)
cpk 200
echo Big balls are protein atoms creating polar interactions with nucleic bases in small furrow
pause
cpk off
select nonpolprot and within(4.5, nonpol_smalldna)
cpk 200
echo Big balls are protein atoms creating hydrophobic interactions with nucleic bases in small furrow
pause
cpk off


