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

set fontsize 12
set fontstroke 1

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 pol_dr *.o5*, *.o4*, *.o3*
echo pol_dr means "polar atoms from deoxyribose"
define pol_ph *.o1p, *.o2p
echo pol_ph means "polar atoms from phosphate-groop"     
define pol_bs_mjg c.n4,a.n6,t.o4,g.o6,g.n7,a.n7
echo pol_bs_mjg means "DNA-base polar atoms from major groove"
define pol_bs_mig c.o2,t.o2,g.n3,g.n2,a.n3
echo pol_bs_mig means "DNA-base polar atoms from minor groove"
echo ***
define npolar_dr dna and backbone and carbon
echo npolar_dr means "not-polar atoms from deoxyribose"
define npolar_ph *.p and dna
echo npolar_ph means "not-polar atoms from phosphate-groop"
define npolar_bs_mig carbon and mig
echo npolar_bs_mig means "DNA-base not-polar atoms from minor groove"
define npolar_bs_mjg carbon and mjg
echo npolar_bs_mjg means "DNA-base not-polar atoms from major groove"

echo ***
define dna_polar pol_dr, pol_ph, pol_bs_mjg, pol_bs_mig
define dna_npolar npolar_dr, npolar_bs_mig, npolar_bs_mjg
echo dna_polar means "all polar atoms from DNA"
echo dna_npolar means "all not-polar atoms from DNA"

select within (3.5,pol_dr) and protein and (*.n???,*.o???)
cpk 200
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,pol_ph) and protein and (*.n???,*.o???)
cpk 200
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,pol_bs_mjg) and protein and (*.n???,*.o???)
cpk 200
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,pol_bs_mig) and protein and (*.n???,*.o???)
cpk 200
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,npolar_dr) and protein and not (*.n???,*.o???)
cpk 200
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,npolar_ph) and protein and not (*.n???,*.o???)
cpk 200
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,npolar_bs_mjg) and protein and not (*.n???,*.o???)
cpk 200
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,npolar_bs_mig) and protein and not (*.n???,*.o???)
cpk 200
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_polar) and protein and (*.n???,*.o???)
cpk 200
color red
echo :)
echo Now you can see all polar-contacts
pause

cpk off
select within (4.5,dna_npolar) and protein and not  (*.n???,*.o???)
cpk 200
color cyan
echo :)
echo Now you can see all hydrophobic-contacts
pause
cpk off