Nazad

set fontsize 8


define mjg  c.n4,a.n6,t.o4,g.o6,g.n7,a.n7,t.c5m,c.c5,g.c8,a.c8,t.c6,c.c6,g.c5,a.c5
define mig  c.o2,t.o2,g.n3,g.n2,a.n3,a.c2
define tocompl t.o4,t.n3,c.n4,c.n3,c.o2,g.o6,g.n1,g.n2,a.n6,a.n1
define basen c.c2,c.c4,c.n1,t.c4,t.c2,t.c5,t.n1,g.c2,g.c4,g.n9,g.c6,a.c4,a.n9,a.c6
define base  mjg,mig,tocompl,basen 

define pad *.o5*, *.o4*, *.o3*
echo pad means "polar atoms from deoxyribose"
define papa *.o1p, *.o2p
echo papa means "polar atoms from phosphate acid"     
define pamjg (oxygen,nitrogen) and mjg 
echo pamjg means "DNA-base polar atoms from major groove"
define pamig (oxygen,nitrogen) and mig 
echo pamig means "DNA-base polar atoms from minor groove"
echo ***
define npad dna and backbone and carbon
echo npad means "not-polar atoms from deoxyribose"
define npapa *.p and dna
echo npapa means "not-polar atoms from phosphate-groop"
define npamig carbon and mig
echo npamig means "DNA-base not-polar atoms from minor groove"
define npamjg carbon and mjg
echo npamjg means "DNA-base not-polar atoms from major groove"

echo ***
define apc pad, papa, pamjg, pamig
define npc npad, npamig, npamjg
echo apc means "all polar atoms from DNA"
echo npc means "all not-polar atoms from DNA"

select within (3.5,pad) and protein and (*.n???,*.o???)
cpk 400
color pink
label %n %r %a %c

echo Polar-contacts of deoxyribose and protein
pause
cpk off
label off

select within (3.5,papa) and protein and (*.n???,*.o???)
cpk 200
color pink
label %n %r %a %c

echo Polar-contacts of phosphate and protein
pause
cpk off
label off

select within (3.5,pamjg) and protein and (*.n???,*.o???)
cpk 200
color pink
label %n %r %a %c

echo polar-contacts of "major groove" and protein
pause
cpk off
label off

select within (3.5,pamig) and protein and (*.n???,*.o???)
cpk 200
color pink
label %n %r %a %c

echo polar-contacts of "minor groove" and protein
pause
cpk off
label off

select within (4.5,npad) and protein and not (*.n???,*.o???)
cpk 200
color purple
label %n %r %a %c

echo Hydrophobic-contacts of deoxyribose and protein
pause
cpk off
label off


select within (4.5,npapa) and protein and not (*.n???,*.o???)
cpk 200
color purple
label %n %r %a %c

echo Hydrophobic-contacts of phosphate and protein
pause
cpk off
label off

select within (4.5,npamjg) and protein and not (*.n???,*.o???)
cpk 200
color purple
label %n %r %a %c

echo Hydrophobic-contacts of atoms from major groove and protein
pause
cpk off
label off

select within (4.5,npamig) and protein and not (*.n???,*.o???)
cpk 200
color purple
label %n %r %a %c

echo Hydrophobic-contacts of atoms from minor groove and protein
pause
cpk off
label off

select within (3.5,apc) and protein and (*.n???,*.o???)
cpk 200
color pink

echo All polar-contacts
pause

cpk off
select within (4.5,npc) and protein and not  (*.n???,*.o???)
cpk 200
color purple

echo All hydrophobic-contacts
pause
cpk off