hide all
select oxygen
var cores = {selected}
ncores = cores.size
scnt = 0
for (var i = 1; i <= ncores; i = i + 1)
   scnt = scnt + 1
   draw ID @{"nuc" + scnt} DIAMETER 80.0  @{cores[i].xyz} COLOR deepskyblue
end for

select elemno=20
var dna = {selected}
ndna = dna.size

scnt = scnt + 1
i =1 
draw ID @{"dna" + scnt} DIAMETER 20.0  @{dna[i].xyz}  COLOR green

for (var i = 2; i <= ndna ; i = i + 1)
   scnt = scnt + 1
   draw ID @{"dna" + scnt} DIAMETER 20.0  @{dna[i].xyz}  COLOR yellow
end for

for (var i = 1; i <= ndna; i=i+2 ) 
  for (var j = i + 2 ; j <= ndna; j=j+2) 
      dis = dna[i].distance(dna[j])
      if (dis < 18) {
            print "  dna-dna " + i + " " + j + " "+ dis
            scnt = scnt + 1
            draw ID @{"sphere" + scnt} DIAMETER 20.0  @{dna[i].xyz}  COLOR red
            scnt = scnt + 1
            draw ID @{"sphere" + scnt} DIAMETER 20.0  @{dna[j].xyz}  COLOR red
	    j = ndna
      }
  end for 
end for

for (var i = 1; i <= ncores; i=i+1 ) 
  for (var j = i + 1 ; j <= ncores; j=j+1) 
      dis = cores[i].distance(cores[j])
      if (dis < 100) {
            print " core-core " + i + " " + j + " "+ dis
            scnt = scnt + 1
            draw ID @{"sphere" + scnt} DIAMETER 80.0  @{cores[i].xyz}  COLOR red
            scnt = scnt + 1
            draw ID @{"sphere" + scnt} DIAMETER 80.0  @{cores[j].xyz}  COLOR red
	    j = ncores
      }
  end for 
end for

for (var i = 1; i <= ndna; i=i+2) 
  for (var j =  1 ; j <= ncores; j=j+1) 
      iddna = @dna[i].atomno
      idcore = @cores[j].atomno
      if((iddna > idcore - 31 ) && ( iddna < idcore)) {
	j =  33 + j 
	print " skipping nuc "
      } else { 
        dis = dna[i].distance(cores[j])
        if (dis < 55) {
            print "  core-dna  " + i + " " + j + " "+ dis
            scnt = scnt + 1
            draw ID @{"sphere" + scnt} DIAMETER 20.0  @{dna[i].xyz}  COLOR red
            scnt = scnt + 1
            draw ID @{"sphere" + scnt} DIAMETER 80.0  @{cores[j].xyz}  COLOR red
	    j = ncores
       }
      }
  end for 
end for