#########################################################################
#                                                                       #
# PyMol Script to render chymotrypsin complexed with inhibitor eglin C  #
# Bird-eyes view at the Ser-His-Asp catalytic triad                     #
#                                                                       #
# Esther Zhuang and Kalju Kahn, UCSB, 2003                              #
#                                                                       #
#########################################################################

hide
select complex, (chain;E,I)
util.ss complex

# General style
set stick_radius=0.15
set sphere_scale=0.3
set cartoon_dumbbell_length,1.40000
set cartoon_dumbbell_radius,0.12000
set cartoon_dumbbell_width,0.15000
set cartoon_cylindrical_helices,0
set cartoon_fancy_helices,1
set cartoon_discrete_colors,1
set cartoon_highlight_color,grey50
set surface_color=gray
set transparency=0.5
set cartoon_smooth_cycles,0

# Show the inhibitor as a green cartoon
select inhib, chain i and (resi 45-46)
show sticks, inhib
cmd.disable('inhib')
set_color green2,[ 0.51, 0.83, 0.31]
color green2, chain i
show cartoon, chain i

# Show the residue of the inhibitor in the active site in spheres
select tease, (c. i and (  (resi 45 and n. O )\
or (resi 45 and n. C ) \
or (resi 45 and n. CB) \
or (resi 46 and n. H ) \
or (resi 46 and n. N )))
show sphere, tease

# Show the catalytic triad in sticks
select active, chain e and (resi 195,102,193,57)
cmd.disable('active')
show sticks, active
color salmon, active
color white, elem h
color hotpink, elem o
color marine, elem n
remove elem h and neighbor elem c

# Hide backbone atoms of the catalytic triad: ugly but worked today.  Note the offset!
cmd.select('lb',"(1ACB_chymotrypsin_h`492)")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`491))) and not (((1ACB_chymotrypsin_h`491)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`494))) and not (((1ACB_chymotrypsin_h`494)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`919))) and not (((1ACB_chymotrypsin_h`919)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`918))) and not (((1ACB_chymotrypsin_h`918)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`2555))) and not (((1ACB_chymotrypsin_h`2555)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`2554))) and not (((1ACB_chymotrypsin_h`2554)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`2558))) and not (((1ACB_chymotrypsin_h`2558)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`2559))) and not (((1ACB_chymotrypsin_h`2559)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`2543))) and not (((1ACB_chymotrypsin_h`2543)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`2546))) and not (((1ACB_chymotrypsin_h`2546)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`1708))) and not (((1ACB_chymotrypsin_h`1708)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`1709))) and not (((1ACB_chymotrypsin_h`1709)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`1710))) and not (((1ACB_chymotrypsin_h`1710)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1ACB_chymotrypsin_h`1727))) and not (((1ACB_chymotrypsin_h`1727)) in (lb)))")
hide sticks, lb

# Show hydrogen bonds within the triad
wizard distance
refresh_wizard
cmd.select('lb',"(1ACB_chymotrypsin_h`916)")
cmd.select('rb',"(1ACB_chymotrypsin_h`493)")
dist
cmd.delete("rb")
cmd.delete("lb")
cmd.select('lb',"(1ACB_chymotrypsin_h`489)")
cmd.select('rb',"(1ACB_chymotrypsin_h`1729)")
dist
cmd.delete("rb")
cmd.delete("lb")
cmd.set_wizard()
cmd.set_wizard()
hide label

# Show chymotrypsin as a transparent surface
create prtn, chain e
set_view (\
     0.617961943,    0.760075629,   -0.201025695,\
     0.190166071,    0.103596121,    0.976272106,\
     0.762864649,   -0.641527653,   -0.080520891,\
     0.000001789,   -0.000000600, -137.444747925,\
     7.046495438,    1.610511661,   17.859127045,\
   102.002891541,  175.874023438,    0.000000000 )
show surface, prtn