#########################################################################
#                                                                       #
# PyMol Script to render haloalkane dehalogenase complexed with DCE     #
# Covalently bound intermediate with nucleophilic water molecule        #
#                                                                       #
# 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 Asp260, His289, Asp124, Trp125, Trp175 in sticks
select active, (resi 260,289,124,125,175)
show sticks, active
hide sticks, elem h and neighbor elem c
color gray, active

# Add hydrogens to the substrate and nucleophilic water
h_add /2DHD_dehal_intermed_xray///312/C1
h_add /2DHD_dehal_intermed_xray///312/C2
h_add /2DHD_dehal_intermed_xray///315/O

# Show covalently bound intermediate and Cl- product
unbond (/2DHD_dehal_intermed_xray///289/HE2), (/2DHD_dehal_intermed_xray///124/OD2),
select inter, resi 312
select product, resi 313
show sticks, inter
show sphere, inter
show sphere, product
color wheat, inter
color yellowgreen, elem cl
color salmon, elem o
color white, elem h
color marine, elem n

# Show nucleophilic water
select water, resi 315
show sticks, water
color oxygen, (water and elem o)

# Hide unimportant atoms
cmd.select('lb',"(2DHD_dehal_intermed_xray`2752)")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`2741))) and not (((2DHD_dehal_intermed_xray`2741)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`2740))) and not (((2DHD_dehal_intermed_xray`2740)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`2754))) and not (((2DHD_dehal_intermed_xray`2754)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`1998))) and not (((2DHD_dehal_intermed_xray`1998)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`1997))) and not (((2DHD_dehal_intermed_xray`1997)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`1981))) and not (((2DHD_dehal_intermed_xray`1981)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`1973))) and not (((2DHD_dehal_intermed_xray`1973)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4519))) and not (((2DHD_dehal_intermed_xray`4519)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4518))) and not (((2DHD_dehal_intermed_xray`4518)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4511))) and not (((2DHD_dehal_intermed_xray`4511)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4510))) and not (((2DHD_dehal_intermed_xray`4510)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4520))) and not (((2DHD_dehal_intermed_xray`4520)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4091))) and not (((2DHD_dehal_intermed_xray`4091)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4083))) and not (((2DHD_dehal_intermed_xray`4083)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4084))) and not (((2DHD_dehal_intermed_xray`4084)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4089))) and not (((2DHD_dehal_intermed_xray`4089)) in (lb)))")
cmd.select('lb',"( ((lb) or ((2DHD_dehal_intermed_xray`4090))) and not (((2DHD_dehal_intermed_xray`4090)) in (lb)))")
cmd.hide("everything","lb")
cmd.disable('lb')

# Show important hydrogen bonds
dist (active and elem h) , (product 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 (\
    -0.212128550,   -0.164355829,   -0.963317454,\
    -0.338507593,    0.937088907,   -0.085340098,\
     0.916741252,    0.307984769,   -0.254418284,\
    -0.000483982,    0.000441326,  -43.081813812,\
    28.717405319,  104.360847473,   30.070455551,\
     9.674826622,   86.161918640,    0.000000000 )

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