zap
echo ""
echo "Now let's look at a different kind of Zn finger protein.  We looked at"
echo "this protein, glucocorticoid receptor, before.  It has two kinds of zinc"
echo " fingers, which serve different purposes.  Hit a key:" 
pause
load pdb "1GLU.PDB"
reset
slab off
rotate z 95
rotate x -82
select *:a
wireframe off
backbone 100
color blue
select *:b
wireframe off
backbone 100
color violet
select 457-469
color yellow
echo ""
echo "Again, the helices interacting with the DNA is shown in yellow."
echo ""
echo "Hit a key to turn on the Zn atoms:"
pause
select zn
spacefill
color white
script "delay1.scr"
script "delay1.scr"
spacefill off
script "delay1.scr"
script "delay1.scr"
spacefill
script "delay1.scr"
script "delay1.scr"
spacefill off
script "delay1.scr"
script "delay1.scr"
spacefill
echo ""
echo "There are two atoms (white) in each subunit, and they serve different"
echo "purposes.  Let's focus on the lower subunit."
pause
select *:b
backbone off
select zn:b
spacefill off
translate y -5
script "delay1.scr"
translate y -10
script "delay1.scr"
translate y -15
script "delay1.scr"
translate y -20
script "delay1.scr"
zoom 125
script "delay1.scr"
zoom 150
script "delay1.scr"
zoom 175
script "delay1.scr"
zoom 200
script "delay1.scr"
translate y -25
script "delay1.scr"
translate y -30
script "delay1.scr"
echo ""
echo "The lower Zn atom serves to organize a zinc finger that gives" 
echo "structure to the alpha helix that contacts the DNA directly"
echo " (shown in yellow and lying in the major groove)" 
echo ""
echo "Hit a key to highlight the zinc finger:"
pause
select 440-470:a
color redorange
echo ""
echo ""
echo "Now let's look at the Zn finger by itself"
pause
select not (440-470:a,zn515:a)
wireframe off
backbone off
spacefill off
echo ""
echo "The alpha helix is pointing out of the screen."
echo "Hit a key to see a ribbon trace and rotate the structure:"
pause
select 440-470:a
ribbons
backbone off
center selected
script "delay1.scr"
script "y-90-2.scr"
script "x90-2.scr"
echo ""
echo "Note that the rest of the finger is a loop, not a beta sheet."
echo "Another difference from the previous protein is that the Zn is"
echo "coordinated by 4 Cys residues, not 2 His and 2 Cys.    Let's "
echo "look at these residues.  First the sulfur atoms (hit a key):"
pause
ribbons off
backbone 50
select within(2.6,zn515:a) and sulfur
color yellow
center selected
spacefill 250
echo ""
echo "The sulfurs (yellow) are located in a tetrahedral arrangement around" 
echo "the Zn. Rotate the molecule as you like.  This will help you see the"
echo "tetrahedral arrangement of the sulfurs. Zoom will help."
echo " Then hit a key to restore the view."
pause
reset
slab off
rotate z -174
rotate y -7
translate x -11
translate y 20
zoom 200
echo ""
echo "Now hit a key to visualize the cysteines." 
pause
select cys and 440-470:a and not 450
wireframe 50
color green
select within(2.6,zn515:a) and sulfur
spacefill 250
center selected
color yellow
echo ""
echo " The cysteines are in two pairs, which are on opposite sides of a loop;"
echo " this organizes the structure. This kind of zinc finger can often be"
echo " identified by this arrangement of cysteines in a protein sequence."
echo ""
echo "Rotate to see the arrangement of Cys's, then hit a key to restore the view:"
pause
reset
slab off
rotate z -174
rotate y -7
translate x -11
translate y 20
zoom 200
select 440-470:a
center selected
echo ""
echo "Hit a key to rotate it:"
pause
script "x-90-2.scr"
script "y90-2.scr"
echo ""
echo "Now return to the entire subunit (hit a key):"
pause
select *:a
color blue
backbone 50
select 440-470:a
color redorange
spacefill off
wireframe off
backbone 50
select zn515:a
color white
select dna
wireframe
echo ""
echo "Now we will look at the other Zn finger.  It has a different"
echo "structure and a different job."
echo ""
echo "The other zinc atom organizes a different part of the protein"
echo " into a dimerization interface.  Hit a key:"
pause
select 474-503:a
color green
select zn516:a
color white
spacefill
script "delay1.scr"
script "delay1.scr"
spacefill off
script "delay1.scr"
script "delay1.scr"
spacefill
script "delay1.scr"
script "delay1.scr"
spacefill off
script "delay1.scr"
script "delay1.scr"
spacefill

echo ""
echo ""
echo ""
echo "This portion of the protein contains two alpha helices."
echo " Hit a key to see them:"
pause
select 474-503:a
ribbons
backbone off
select 492-503:a
color greenblue
echo ""
echo "The two helices are colored slightly differently. "
echo "Hit a key for a better view of the helices:"
pause
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x 5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
script "delay1.scr"
rotate x -5
echo ""
echo "Now turn on the upper subunit (any key):"
pause
select zn:b
color white
spacefill
select *:b and not zn
backbone
color violet
select 474-503:b
backbone off
ribbons
color magenta
echo ""
echo "The region of contact between the two subunits is visible."
echo "Rotate it to see it better (any key):"
pause
rotate y 5
script "delay1.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"
rotate y 5
script "delay1.scr"
echo ""
echo "Hit a key to turn on spacefill:"
pause
select protein
spacefill
echo ""
echo ""
echo "This shows that the dimerization interface is closely packed."
echo "Hit a key:"
pause
rotate y -5
script "delay1.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"
rotate y -5
script "delay1.scr"
echo ""
echo "Hit a key to turn off spacefill:"
pause
spacefill off
echo ""
echo "Now return to the original view"
pause
translate y -15
script "delay0.scr"
translate y -10
script "delay0.scr"
translate y -5
script "delay0.scr"
translate y 0
script "delay0.scr"
zoom 180
script "delay0.scr"
zoom 160
script "delay0.scr"
zoom 140
script "delay0.scr"
zoom 125
script "delay0.scr"
zoom 112
script "delay0.scr"
zoom 100
script "delay1.scr"
echo ""
echo "Hit a key to give the original depiction:"
pause
select *:a
backbone 100
ribbons off
color blue
select *:b
backbone 100
color violet
ribbons off
select zn
color white
script "delay1.scr"
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 ""
echo "Hit a key to look at another kind of zinc finger protein:"
pause90