#########################################################################
#                                                                       #
# PyMol Script to render alpha helix                                    #
# Showing backbone in ball and stick with hydrogen bonds                #
#                                                                       #
# Esther Zhuang and Kalju Kahn, UCSB, 2003                              #
#                                                                       #
#########################################################################

hide

# Set general style
set sphere_scale, 0.25000
set stick_radius, 0.15000
set dash_radius, 0.1

# Define and display the alpha helix
select helix, resi 88-99
select backbone, (name ca or name c or name o or name n or name h)

show sticks, helix and backbone
show spheres, helix and (name o or name h)
color gray

cmd.dss("1H6M_b_turn")
show cartoon, helix 
cartoon loop

color oxygen, name o
color marine, name n
color white, name h

# Display hydrogen bonds
dist (helix and name o), (helix and (name h and neighbor name n)), 2.485
hide label

# Hide unimportant atoms at the ends
cmd.select('lb',"(1H6M_b_turn`1490)")
cmd.select('lb',"( ((lb) or ((1H6M_b_turn`1489))) and not (((1H6M_b_turn`1489)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1H6M_b_turn`1325))) and not (((1H6M_b_turn`1325)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1H6M_b_turn`1317))) and not (((1H6M_b_turn`1317)) in (lb)))")
cmd.hide("everything","lb")
cmd.disable('lb')

show sticks, helix
hide cartoon
cmd.show("ribbon"    ,"helix")
set stick_radius=0.1
color oxygen, elem o
color marine, elem n
color orange, elem s
hide sticks, elem h and neighbor elem c
set ribbon_width,0.20000
set ribbon_radius,0.20000
color white, elem h
cmd.delete("lb")
cmd.select('lb',"(1H6M_b_turn`1472)")
cmd.select('lb',"( ((lb) or ((1H6M_b_turn`1451))) and not (((1H6M_b_turn`1451)) in (lb)))")
hide sphere, lb
cmd.delete("lb")
cmd.select('lb',"(1H6M_b_turn`1370)")
cmd.select('lb',"( ((lb) or ((1H6M_b_turn`1346))) and not (((1H6M_b_turn`1346)) in (lb)))")
remove lb
cmd.delete("lb")
cmd.select('lb',"(1H6M_b_turn`1343)")
cmd.select('lb',"( ((lb) or ((1H6M_b_turn`1357))) and not (((1H6M_b_turn`1357)) in (lb)))")
hide sphere, lb
cmd.disable('lb')
_ set_view (\
_    -0.840123415,   -0.034430176,    0.541276217,\
_    -0.376906931,   -0.680562198,   -0.628296196,\
_     0.390010536,   -0.731866062,    0.558785260,\
_    -0.000143722,    0.000577497,  -66.268577576,\
_    -4.929811954,   15.754426003,   22.490634918,\
_    40.512248993,   99.521148682,    0.000000000 )