#########################################################################
#                                                                       #
# 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')

# Zoom into the helix
set_view (\
    0.740355968,   -0.009942315,   -0.672144771,\
    0.420057178,   -0.773792148,    0.474130332,\
   -0.524813890,   -0.633361936,   -0.568706512,\
   -0.000017107,   -0.000012091,  -56.465415955,\
   -7.134911060,   18.095998764,   20.566793442,\
   30.712228775,   89.721076965,    0.000000000 )

util.performance(0)
ray