#!rasmol -script
# File: NUC1.SPT
# Creator: RasMol Version 2.6

zap
background [0,0,0]
load pdb "NUC-SOME.PDB"
set ambient 60
set specular off
define h3 *:a,*:e
define h4 *:b,*:f
define h2a *:c,*:g
define h2b *:d,*:h
select dna
wireframe off
backbone 300
color blue
select protein
wireframe off
ribbons
select dna and (2,292,146,148) and *.p
Color white
select dna and (3,291,145,149) and *.p
Color [100,200,255]
select dna and (4,290,144,150) and *.p
Color [50,150,255]
select dna and (5, 289, 143,151) and *.p
Color [0,100,255]
rotate x 5
echo ""
echo "The ends of the DNA are lighter blue to help visualize them."
Echo "      Hit a key to rotate the structure:"
pause
script "x-90-2.scr"
echo ""
echo "Note that the structure is in two layers."
script "y90-2.scr"
script "y90-2.scr"
script "y90-2.scr"
echo ""
echo "rotate as you like, then hit a key to restore"
echo ""
pause
reset
slab off
rotate z 90
rotate y -5
rotate x -90
echo ""
echo "Now let's look at the protein.  Hit a key:"
pause
restrict protein

select h3
color red
select h4
color [255,100,0]
select h2a
color green
select h2b
color greenblue
script x90-2.scr
echo ""
echo "The protein is made up of two layers.  Hit a key to focus on one:"
pause
restrict *:a,*:b,*:c,*:d
echo ""
echo "Each layer has two heterodimers, one of H3:H4 and one of H2A:H2B."
Echo "Hit a key to make H3:H4 blink:"
pause
select *:a,*:b
ribbons off
script delay1.scr
ribbons on
script delay1.scr
ribbons off
script delay1.scr
ribbons on
script delay1.scr
ribbons off
script delay1.scr
ribbons on
script delay1.scr
ribbons off
script delay1.scr
ribbons on
echo ""
echo "Now let's look at the two H3:H4 heterodimers:"
pause
restrict h3,h4
ribbons on
echo ""
echo "Hit a key to rotate:"
pause
script x90-2.scr


# this makes something blink:
#script "delay1.scr"
#spacefill 150
#script "delay1.scr"
#spacefill off
#script "delay1.scr"
#spacefill 150