zap
echo "We find recurring structural motifs in many DNA-binding proteins." 
echo "      This script will examine some of these common motifs."
echo ""
echo "Hit a key to continue."
pause
load "1lmb.pdb"
define ab (*.n9,*.c8,*.n7,*.c5,*.c6,*.n6,*.n1,*.c2,*.n3,*.c4)
define cb (*.n1,*.c2,*.o2,*.n3,*.c4,*.n4,*.c5,*.c6)
define gb  (*.n9,*.c8,*.n7,*.c5,*.c6,*.o6,*.n1,*.c2,*.n2,*.n3,*.c4)
define tb  (*.n1,*.c2,*.o2,*.n3,*.c4,*.o4,*.c5,*.c5m,*.c6)
define ade17 a17:1 and ab
define ade24 a24:2 and ab
define gua16 g16:1 and gb
define thy18 t18:1 and tb
define cyt26 c26:2 and cb
define thy25 t25:2 and tb
slab off
rotate z 2
rotate y -58
rotate x -64
zoom 96
select protein
wireframe off
ribbons
select *:4
color green
select *:3
color yellow
select dna
wireframe 50
color blue
echo ""

echo ""
echo "This protein is the phage lambda CI repressor.  It binds to the DNA"
echo " as a dimer.  The two protein subunits are colored green and yellow."
echo ""
echo "Hit a key to continue."
pause
echo ""
echo "The motif used in this protein is a helix-turn-helix (HTH) motif."
echo " In each subunit, the HTH is colored red.  Though it looks "
echo " somewhat separate from the rest of the protein in this diagram,"
echo " its structure is actually integrated into that of the rest of the protein."
echo " Hit a key to see a spacefilling representation:"
select protein and 33-51
color red
pause
select protein
spacefill
echo ""
echo "Hit a key for a cross-section:"
pause
echo ""
echo "Clearly the HTH motif is not a domain separate from the rest of the protein."
echo ""
echo "Hit a key to remove the spacefill"
slab 55
pause
slab off
spacefill off
echo ""
echo "Now let's look more closely at the HTH motif (hit a key)."
pause
restrict protein and 33-51 and *:4
center selected
backbone off
slab off
#rotate z 27
#rotate y -60
#rotate x -44
#translate x 42
#translate y 18
script "zoomhth1.txt"
restrict *:4 and 33-51
select *:4 and 33-51
center selected
backbone off
wireframe off
script "delay1.scr"
echo ""
echo "In this representation, the helices are represented by ribbons."
echo " The HTH consists of two helices, separated by a short stretch of "
echo "  non-helical material (the turn).  Hit a key to color the turn purple"
pause
select *:4 and 40-43
color purple
echo ""
echo "The bottom helix is often called the recognition helix, and it makes"
echo "   the specific contacts with the DNA. Hit a key to turn it blue. "
pause
select *:4 and 44-51
color blue
echo ""
echo "Hit a key to rotate the molecule."
pause
select *:4 and 33-51
backbone off
ribbons
echo ""
echo "Note that, as the structure rotates, it seems very spacious,"
echo "but actually the two helices are packed tightly together."
echo "This helps fix the position of the recognition helix relative"
echo "to the helix above.  Hit a key to see the packing:" 
script "y90-2.scr" 
pause
spacefill
echo ""
echo "The tight packing helps anchor the recognition helix relative to"
echo " the rest of the protein, so that its relationship to the DNA is fixed. "
script "y-90-2.scr" 
echo ""
echo "Hit a key to turn off spacefill"
pause
spacefill off
echo ""
echo "Hit a key to turn on two of the side chains that interact with the DNA"
pause
select *:4 and (44,45) 
wireframe 75
color green
select *:4 and (44,45) and backbone
color blue
echo ""
echo "Note that the side chains project away from the protein towards the DNA,"
echo " which lies below the protein in this view."
echo ""
echo "Hit a key to turn on two of the DNA bases that contact the protein"
pause
select ade24, gua16
color orange
wireframe 60
monitor 482 1835
monitor 485 1834
monitor 322 1841
monitor 319 1841
echo "Note the hydrogen bonds between the protein and the DNA."
script "delay1.scr"
script "delay1.scr"
script "y90-2.scr" 
script "delay1.scr"
script "y-90-2.scr" 
echo ""
echo "Hit a key to show a few more of the bases"
pause
select ade17,thy18,thy25,cyt26
color purple
wireframe 60
monitor 526 322
monitor 524 323
monitor 523 325
monitor 365 485
monitor 363 486
monitor 344 506
monitor 345 504
echo ""
echo "Now we see the complementary bases to the two shown in orange,"
echo "and the base pair lying between the two that are contacted."
echo ""
echo "Rotate as you like; observe the planes of the base pairs."
echo " When done, hit a key to return to previous view"
pause
reset
#rotate z 27
#rotate y -60
#rotate x -44
#translate x 73
#translate y 18
#zoom 311

rotate z 8
rotate y -61
rotate x -29
translate x 72
translate y 5
zoom 311

echo "Hit a key to turn on the DNA"
pause
monitor off
select dna
color blue
wireframe 50
select *:4 and 33-51
color red
script "zoomout1.txt"
echo ""
echo "Hit a key to turn on the protein; it has two subunits, each with an HTH."
pause
select *:4 
ribbons
color green 
select *:3
ribbons
color yellow
select (*:4 ,*:3) and (33-51)
color red
wireframe off
echo ""
echo "Again note that the HTH motifs (in red) are is only a small part" 
echo " of the protein, not a separate domain.  Hit a key to rotate the complex."
pause
script "x90-2.scr"
select protein
spacefill
script "delay1.scr"
script "x-90-2.scr"
spacefill off
echo ""
echo "Finally let's see how the HTH relates to the grooves in the DNA."
pause
select protein
ribbons off
select protein and 33-51
ribbons
rotate y-1
script "delay1.scr"
rotate y-1
script "delay1.scr"
rotate y-1
script "delay1.scr"
rotate y-1
script "delay1.scr"
rotate y-1
script "delay1.scr"
rotate y-1
script "delay1.scr"
echo ""
echo "Note how the alpha helix lies in the major groove of the DNA"
echo "and parallel to the groove at that point.  We will see this feature"
echo "in many protein-DNA complexes.  Manipulate the structure as you like."