#########################################################################
#                                                                       #
# PyMol Script to render haloalkane dehalogenase complexed with DCE     #
# Boeund substrate with two tryptophans near leaving halogen            #
#                                                                       #
# Esther Zhuang and Kalju Kahn, UCSB, 2003                              #
#                                                                       #
#########################################################################

hide

# General style
set stick_radius, 0.20
set sphere_scale, 0.35
set dash_radius, 0.1

# Show active site residues Asp124, Trp125, Trp175 in sticks
select active, (resi 124,125,175)
show sticks, active
hide sticks, elem h and neighbor elem c
color gray, active
color oxygen, elem o
color marine, elem n

# Add hydrogens to the substrate
cmd.select('lb',"(2DHC_dehal_substrate_xray`4867)")
h_add lb
cmd.delete("lb")
cmd.select('lb',"(2DHC_dehal_substrate_xray`4866)")
h_add lb
cmd.delete("lb")

# Show the bound substrate in ball and stick
select sub, resi 312
show sticks, sub
show sphere, sub
color wheat, sub
color yellowgreen, elem cl
color white, elem h

# Hide unimportant atoms of active site residues using mouse selection
cmd.select('lb',"(2DHC_dehal_substrate_xray`2740)")
cmd.select('lb',"( ((lb) or ((2DHC_dehal_substrate_xray`2741))) and not (((2DHC_dehal_substrate_xray`2741)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHC_dehal_substrate_xray`2752))) and not (((2DHC_dehal_substrate_xray`2752)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHC_dehal_substrate_xray`2753))) and not (((2DHC_dehal_substrate_xray`2753)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHC_dehal_substrate_xray`1998))) and not (((2DHC_dehal_substrate_xray`1998)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHC_dehal_substrate_xray`1997))) and not (((2DHC_dehal_substrate_xray`1997)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHC_dehal_substrate_xray`1981))) and not (((2DHC_dehal_substrate_xray`1981)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHC_dehal_substrate_xray`1973))) and not (((2DHC_dehal_substrate_xray`1973)) in (lb)))")
cmd.hide("everything","lb")
cmd.delete("lb")

# Show important hydrogen bonds
dist (active and elem h) , (sub and elem cl), 3.00
dist (active and elem h) , (active and elem o), 2.30
hide label

# Zoom into the active site
set_view (\
     0.138596892,   -0.968074143,   -0.208865270,\
    -0.487367481,    0.116922237,   -0.865332007,\
     0.862127662,    0.221726626,   -0.455603540,\
     0.000188485,   -0.000142777,  -36.038719177,\
    28.987277985,  103.712936401,   31.076498032,\
     2.739213943,   79.080062866,    0.000000000 )

util.performance(0)
util.ray_shadows('none')
ray