#############################################################################
#                                                                           #
# PyMol Script to render chymotrypsin complexed with a synthetic inhibitor  #
# Close-up view at the hydrophobic binding pocket                           #
#                                                                           #
# Esther Zhuang and Kalju Kahn, UCSB, 2003                                  #
#                                                                           #
#############################################################################

hide

# General style
set stick_radius=0.15
set sphere_scale=0.17
set surface_color=gray
set transparency=0.27

# Show the inhibitor as sticks and spheres
select inhi, chain d or ((resi 241-242) and (!chain c))
show sticks, inhi
show sphere, inhi
color forest, inhi
cmd.disable('inhi')

# Show the hydrophobic pocket
select pocket, (resi 192,191,220,219,189,218,217,216,215,226,227,214)
show sticks, pocket
color yellow, pocket
cmd.disable('pocket')


# Show the catalytic triad in sticks
select active, (resi 57,195,102)
show sticks, active
hide sticks, resi 57 and (name HE2)
hide sticks, resi 57 and (name H)
hide sticks, resi 57 and (name O)
hide sticks, resi 102 and (name H)
hide sticks, resi 102 and (name O)
hide sticks, resi 195 and (name H)
hide sticks, resi 195 and (name O)
color marine, active
cmd.disable('active')

# Hide nonpolar hydrogens
select h, elem h and (neighbor elem c)
hide sticks, h
hide sphere, h
cmd.disable('h')

# Show protein in transparent surface
set_view (\
    -0.065684743,   -0.700858772,    0.710269809,\
     0.088670596,   -0.713091433,   -0.695441663,\
     0.993892968,    0.017299812,    0.108983852,\
     0.000006177,   -0.000049647,  -72.166511536,\
    22.503955841,   10.081019402,   40.355175018,\
    42.956813812,  109.890396118,    0.000000000 )

create prtn, (chain a,b,c)
show surface, prtn

# Suggested raytracing options
#set ambient,0.30000
#set spec_reflect,0.36000