# Этот скрипт - для исследования контактов между молекулами белка и ДНК

set fontsize 5
set fontstroke 0

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 
echo mjg means "DNA base  atoms from major groove"
echo mig means "DNA base  atoms from minor groove"
echo base="dna and not backbone"
echo ***

define p_d *.o5*, *.o4*, *.o3*
echo p_d means "polar atoms from deoxyribose"
define p_h *.o1p, *.o2p
echo p_h means "polar atoms from phosphate-groop"     
define p_mjg c.n4,a.n6,t.o4,g.o6,g.n7,a.n7
echo p_mjg means "DNA-base polar atoms from major groove"
define p_mig c.o2,t.o2,g.n3,g.n2,a.n3
echo p_mig means "DNA-base polar atoms from minor groove"
echo ***
define n_d dna and backbone and carbon
echo n_d means "not-polar atoms from deoxyribose"
define n_p *.p and dna
echo n_p means "not-polar atoms from phosphate-groop"
define n_mig carbon and mig
echo n_mig means "DNA-base not-polar atoms from minor groove"
define n_mjg carbon and mjg
echo n_mjg means "DNA-base not-polar atoms from major groove"

echo ***
define dna_p p_d, p_h, p_mjg, p_mig
define dna_n n_d, n_mig, n_mjg
echo dna_p means "all polar atoms from DNA"
echo dna_n means "all not-polar atoms from DNA"

select within (3.5,p_d) and protein and (*.n???,*.o???)
cpk 400
color red
label %n %r %a %c
echo :)
echo Now you can see  polar-contacts of deoxyribose and protein
pause
cpk off
label off

select within (3.5,p_h) and protein and (*.n???,*.o???)
cpk 400
color red
label %n %r %a %c
echo :)
echo Now you can see  polar-contacts of phosphate and protein
pause
cpk off
label off

select within (3.5,p_mjg) and protein and (*.n???,*.o???)
cpk 400
color red
label %n %r %a %c
echo :)
echo Now you can see  polar-contacts of "major groove" and protein
pause
cpk off
label off

select within (3.5,p_mig) and protein and (*.n???,*.o???)
cpk 400
color red
label %n %r %a %c
echo :)
echo Now you can see  polar-contacts of "minor groove" and protein
pause
cpk off
label off

select within (4.5,n_d) and protein and not (*.n???,*.o???)
cpk 400
color cyan
label %n %r %a %c
echo :)
echo Now you can see  hydrophobic-contacts of deoxyribose and protein
pause
cpk off
label off


select within (4.5,n_p) and protein and not (*.n???,*.o???)
cpk 400
color cyan
label %n %r %a %c
echo :)
echo Now you can see  hydrophobic-contacts of phosphate and protein
pause
cpk off
label off

select within (4.5,n_mjg) and protein and not (*.n???,*.o???)
cpk 400
color cyan
label %n %r %a %c
echo :)
echo Now you can see  hydrophobic-contacts of atoms from major groove and protein
pause
cpk off
label off

select within (4.5,n_mig) and protein and not (*.n???,*.o???)
cpk 400
color cyan
label %n %r %a %c
echo :)
echo Now you can see  hydrophobic-contacts of atoms from minor groove and protein
pause
cpk off
label off

select within (3.5,dna_p) and protein and (*.n???,*.o???)
cpk 400
color red
echo :)
echo Now you can see all polar-contacts
pause

cpk off
select within (4.5,dna_n) and protein and not  (*.n???,*.o???)
cpk 400
color cyan
echo :)
echo Now you can see all hydrophobic-contacts
pause
cpk off