zap
load "1glu.pdb"
define gua4 g4:c and (*.n9,*.c8,*.n7,*.c5,*.c6,*.o6,*.n1,*.c2,*.n2,*.n3,*.c4)
define guamin7 g-7:d and (*.n9,*.c8,*.n7,*.c5,*.c6,*.o6,*.n1,*.c2,*.n2,*.n3,*.c4)
define thy6 t6:c and (*.n1,*.c2,*.o2,*.n3,*.c4,*.o4,*.c5,*.c5m,*.c6)
echo ""
echo "We will first look at a typical DNA-binding protein bound to its site" 
echo "for an overview of these complexes."
echo "This is the complex of glucocorticoid receptor with its binding site."
echo "Hit a key for a better view"
pause
script "x-90-2.scr"
script "y-90-2.scr"
echo ""
echo "It's still relatively complicated."
echo "Lets look at the parts separately:  First the DNA.  Note"
echo "the differing sizes of the major and minor grooves:"
pause
restrict dna
center selected
script "y-90-2.scr"
spacefill 200
script "y-90-2.scr"
spacefill 
script "y-90-2.scr"
spacefill off
wireframe 50
script "y-90-2.scr"
echo ""
echo "Now turn on the protein.  The bound form of this protein, like most "
echo "DNA-binding proteins, is a dimer.  The monomers are in two colors:"
pause
select *:a
wireframe
color blue
select *:b
wireframe
color violet
echo ""
echo "It's still complicated.  Simplify the protein (hit a key):"
pause
select *:a,*:b
wireframe off
backbone 100
echo ""
echo ""
echo "Now we have a backbone trace."
echo ""
echo "RasMol allows many different representations. Here is spacefilling:"
pause
spacefill
backbone off
echo ""
echo "And it can display secondary structure"
pause
spacefill off
ribbons
echo ""
echo "Any key to return to the backbone trace:"
pause
ribbons off
backbone 100
echo ""
echo "Hit a key; it will switch to spacefill to emphasize 3 points:"
echo "  First, the protein lies on one side of the DNA helix."
echo "  Second, the protein and the DNA are about the same size."
echo "  Third, there is close contact between the protein and the DNA."
pause
script "y-90-2.scr"
select dna,protein
spacefill 
script "y-90-2.scr"
echo "Hit a key to continue:"
pause
script "y-90-2.scr"
spacefill off
script "y-90-2.scr"

echo ""
echo "Now let's look at a feature of most DNA-binding proteins:"
echo "  In various ways, they place an alpha helix in the major groove"
echo "   of the DNA.  Hit a key:"
pause
select 457-469
color yellow
echo ""
echo "The alpha helices that lie in the major groove are highlighted in yellow."
echo ""
echo "Hit a key for a better view"
pause
rotate x 2
script "delay0.scr"
rotate x 2
script "delay0.scr"
rotate x 2
script "delay0.scr"
rotate x 2
script "delay0.scr"
rotate y -2
script "delay0.scr"
rotate y -2
script "delay0.scr"
rotate y -2
script "delay0.scr"
echo ""
echo "Note how the helices fit nicely into the major groove"
echo "To see that they fill the groove, hit a key:"
pause
spacefill
select dna
spacefill
echo ""
echo "This can be visualized by taking cross-sections."
echo "First stain the DNA red (hit a key)."
pause
color red
echo ""
echo "Now it will show cross-sections, moving from back to front."
echo "Pay attention to the interface between the protein (yellow)"
echo "and the DNA (red) for the lower subunit."
pause
script "grslab.txt"