Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/~ogion/projects/DP-cont/dna_full.txt Дата изменения: Thu Dec 27 11:37:31 2007 Дата индексирования: Tue Oct 2 11:14:53 2012 Кодировка:

set fontstroke 2
Echo THIS SCRIPT IS DESIGND FOR STYING DNA-PROTEIN CONTACTS IN THIS STRUCTURE. SCRIPT SHOWS STEP BY STEP SOME TYPES OF THIS CONTACTS. YOU MAY MEASURE DISTANCES BETWEEN ANY ATOMS IN PAUSES OF SCRIPT'S WORK.
restrict none
select C422C.P
label THIS SCRIPT IS DESIGND FOR STYING DNA-PROTEIN CONTACTS IN THIS STRUCTURE
pause
label SCRIPT SHOWS STEP BY STEP SOME TYPES OF THIS CONTACTS
pause
label YOU MAY MEASURE DISTANCES BETWEEN ANY ATOMS IN PAUSES OF SCRIPT'S WORK
pause
#-----defining parts of dna
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

#---------------defining polar and nonpolar atoms of protein
define protpol (elemno=8 | elemno= 7) & protein
define protnonpol (protein & ! protpol)

#--------defining polar & nonpolar atoms of backbone
define derib_pol *.O?*
define derib_np *.C?*
define p_pol *.O?P & ! protein

#---------defining polar & nonpolar atoms of major & minor grooves
define mjg_pol (oxygen,nitrogen) & mjg
define mig_pol (oxygen,nitrogen) & mig
define mjg_np carbon & mjg
define mig_np carbon & mig

#---------let us look on contacts
echo ---Here we see full structure with protein & both chains of dna---
restrict none
select all
wireframe 40
spacefill off
color cpk
pause

echo ---Here is DNA---
select *B
color Yellow
wireframe 50
select *C
color Green
wireframe 50
set picking distance
pause

echo ---Here is Protein---
select protein
colour blue
wireframe 50
select *B
color cpk
select *C
color cpk
color cpk
set picking distance
pause

echo ---Here is polar atoms of protein---
select protpol
color cpk
spacefill 100
set picking distance
pause

echo ---Here is nonpolar atoms of protein---
restrict none
select protein
colour blue
wireframe 50
select *B
color cpk
wireframe 50
select *C
color cpk
wireframe 50
select protnonpol
color cpk
spacefill 100
set picking distance
pause

select all
color cpk

#----------polar contacts of desoxyribose & protein
echo ---Polar contacts of desoxyribose & protein---
label off
restrict none
select all
wireframe
spacefill off
select *B
color Yellow
select *C
color Green
select protein
colour blue

select derib_pol
spacefill 100

select within (3.5, derib_pol) & protpol
label %e
spacefill 200
define p1 selected
select within (3.5, p1) & derib_pol
spacefill 200
label %e
set picking distance

pause

#----------nonpolar contacts of desoxyribose & protein
echo ---Nonpolar contacts of desoxyribose & protein---
label off
restrict none
select all
wireframe
spacefill off
select *B
color Yellow
select *C
color Green
select protein
colour blue

select derib_np
spacefill 100

select within (4.5, derib_np) & protnonpol
label %e
spacefill 200
define p2 selected
select within (4.5, p2) & derib_np
spacefill 200
set picking distance
label %e
pause

#----------polar contacts of phosphate & protein
echo ---Polar contacts of phosphate & protein---
label off
restrict none
select all
wireframe
spacefill off
select *B
color Yellow
select *C
color Green
select protein
colour blue

select p_pol
spacefill 100

select within (3.5, p_pol) & protpol
label %e
spacefill 200
define p3 selected
select within (3.5, p3) & p_pol
spacefill 200
set picking distance
label %e
pause

#----------Polar contacts of major groove atoms & protein
echo ---Polar contacts of major groove atoms & protein---
label off
restrict none
select all
wireframe
spacefill off
select *B
color Yellow
select *C
color Green
select protein
colour blue

select mjg_pol
spacefill 100

select within (3.5, mjg_pol) & protpol
label %e
spacefill 200
define p4 selected
select within (3.5, p4) & mjg_pol
spacefill 200
set picking distance
label %e
pause

#----------Nonolar contacts of major groove atoms & protein
echo ---Nonpolar contacts of major groove atoms & protein---
label off
restrict none
select all
wireframe
spacefill off
select *B
color Yellow
select *C
color Green
select protein
colour blue

select mjg_np
spacefill 100

select within (4.5, mjg_np) & protnonpol
label %e
spacefill 200
define p5 selected
select within (4.5, p5) & mjg_np
spacefill 200
set picking distance
label %e
pause

#----------Polar contacts of minor groove atoms & protein
echo ---Polar contacts of minor groove atoms & protein---
label off
restrict none
select all
wireframe
spacefill off
select *B
color Yellow
select *C
color Green
select protein
colour blue

select mig_pol

spacefill 100
select within (3.5, mig_pol) & protpol
label %e
spacefill 200
define p6 selected
select within (3.5, p6) & mig_pol
spacefill 200
set picking distance
label %e
pause

#----------Nonpolar contacts of minor groove atoms & protein
echo ---Nonolar contacts of minor groove atoms & protein---
label off
restrict none
select all
wireframe
spacefill off
select *B
color Yellow
select *C
color Green
select protein
colour blue

select mig_np

spacefill 100
select within (4.5, mig_np) & protnonpol
label %e
spacefill 200
define p7 selected
select within (4.5, p7) & mig_np
spacefill 200
set picking distance
label %e
pause