#Script for presentation of alpha helix geometry
#If you don't have the molecule loaded, you will need to...
#load ideal_alpha.pdb
#Commands start here.  If cutting and pasting, select chunks up
#to each pause
cartoons
select all
color cpk
select *.CA
color group
#
echo "This shows the cartoon view, with blue at the N-terminus"
echo "Press any key to continue"
pause
# (For some reason the pause/wait command no longer works in recent versions
#  of Rasmol, but the error message is harmless)
color ribbon none
select all
color white
restrict 42-54
set hbonds sidechain
hbonds 50
color hbonds green
color cpk
select 42-54 and *.CA
color group
ribbons off
backbone 100
center 48
translate y 0
translate x 0
zoom 350
select 42-54
wireframe 25
#
echo "Now we've zoomed in on a short segment.  H-bonds along"
echo "  backbone are in green"
echo "Press any key to continue"
pause
#
color shapely
select 42-54 and *.CA
spacefill 250
label %n
set fontsize 16
select 42,46,50,54
wireframe 100
#
echo "Every fourth side chains lines up on one side"
echo "Press any key to continue"
pause
#
select 42-54
spacefill
#
echo "Spacefill the whole thing"
echo "Press any key to continue"
pause
#
spacefill off
select 42-54 and *.CA
spacefill 250
select 42-54 and backbone
color cpk
wireframe 100
set hbonds sidechain
label off
reset
zoom 350
center 48
rotate z 7
rotate y -5
rotate x 44
translate x 60
translate y -82
ribbons 150
#
echo "Trace H-bond connectivity"
echo "The end"
#