zap
load "gcn4.pdb"
slab off
rotate z -105
rotate y 84
rotate x -169
zoom 96
select dna
color blue
select protein
wireframe off
ribbons
select 229-290 and *:c
color green
select 229-290 and *:d
color yellow
echo ""
echo "This is a typical 'basic leucine-zipper' or 'bZIP' protein, GCN4 of yeast." 
echo " The DNA is in blue.  Again, the protein is a dimer, with the subunits"
echo "colored differently. " 
echo ""
echo "Hit a key to change the coloring scheme:"
pause
select 229-249 and protein
color orange
select 250-290 and protein
color red
echo ""
echo "Each subunit is a long alpha helix, but different parts of the helix"
echo "have different functions.   The DNA-binding portion (orange) is called"
echo "the basic region; the upper part (red) is a protein dimerization motif called"
echo " a leucine zipper.  The helices from each subunit wrap gently around each"
echo " other in a structured called a coiled-coil. Hit a key to rotate the complex."
pause
script "x90-2.scr"
script "delay1.scr"
script "x-90-2.scr"
echo ""
echo "The DNA-binding portion of the protein is colored orange, and is"
echo " called the 'basic region' because it is rich in basic amino acids." 
echo " Note that it is also alpha-helical, and is an extension of the" 
echo " dimerization motif.  Hit a key to look closer:"
pause
zoom 150
translate y-10
restrict dna,229-249
echo ""
echo ""
echo "Hit a key to rotate the complex."
pause
script "x90-2.scr"
rotate y 5
script "delay1.scr"
rotate y 5
script "delay1.scr"
rotate y 5
script "delay1.scr"
rotate y 5
script "delay1.scr"
echo ""
echo "Note that, as with the other proteins, the alpha helix of the basic region"
echo " lies in the major groove.  Hit a key to restore the original view."
pause
reset
rotate z -105
rotate y 84
rotate x -169
zoom 96
select protein
ribbons
echo ""
echo "Now look at the coiled-coil:"
pause
zoom 150
script "delay1.scr"
restrict 220-290
script "basiczap.txt"
restrict 250-290 #can comment previous line
center selected
script "delay1.scr"
translate y 10
script "delay1.scr"
translate y 20
script "delay1.scr"
translate y 30
script "delay1.scr"
translate y 40
echo "Hit a key to rotate"
pause
echo ""
echo "Note how the helices wrap about one another"
script "x90-2.scr"
echo ""
echo "Hit a key to look at the leucines that give the zipper its name"
pause
select 250-275 and leu
color blue
wireframe 75
rotate z 20
script "delay1.scr"
zoom 160
script "delay1.scr"
zoom 170
 script "delay1.scr"
zoom 180 
script "delay1.scr"
zoom 190 
script "delay1.scr"
echo ""
echo "The leucines are in every seventh position in the protein; that is,two turns"
echo " apart in the alpha helix.  This places them on the same side of the helix."
echo "  Note how the leucines from the two helices interact with each other."
script "x-90-2.scr"
echo ""
echo "Hit a key to make the structure spacefilled."
pause
echo ""
echo " The leucines lie at the interface between the helices,"
echo "    and are mostly not visible."
select 250-290
spacefill
script "x90-2.scr"
echo "Hit a key to view a cross-section at various levels."
pause
echo ""
echo "Note how the leucines pack against one another, and are on the inside."
script "slabber1.scr"
echo ""
echo "Hit a key to remove the spacefill."
pause
spacefill off
echo "Manipulate the image to see how the helices wrap around each other,"
echo "and how the leucines pack against one another."
echo "When done, hit a key to restore the image."
pause
reset
spacefill off
slab off
rotate z 63
rotate y 52
rotate x 4
translate x -1
translate y 40
zoom 150