#########################################################################
#                                                                       #
# PyMol Script to render carboxypeptidase active site                   #
# Showing zinc coordination and bound ligand                            #
#                                                                       #
# Esther Zhuang and Kalju Kahn, UCSB, 2003-2004                         #
#                                                                       #
#########################################################################

hide 

# General style
set sphere_scale, 0.15
set stick_radius, 0.1
set dash_radius, 0.1

# Show active site residues His69, Glu72, Asn144, Arg145, His196, and Glu 270
select active, (resi 69,72,144,145,196,270)
show sticks, active
color gray, active
hide sticks, elem h and neighbor elem c
cmd.disable('active')

# Show bound ligand (Aminocarbonylphenylalanine)
select sub, resi 310
show sticks, sub
show sphere, sub
color yellowgreen, sub
color marine, elem n
color salmon, elem o
color white, elem h
hide sticks, elem h and neighbor elem c
cmd.disable('sub')

# Show catalytic zinc ion
show sphere, elem zn
color hotpink, elem zn

# Show coordination to zinc and hydrogen bonds in the active site
dist (elem zn) , (sub and elem o), 2.40
dist (elem zn) , (active and elem o), 2.40
dist (elem zn) , (active and elem n), 2.40
dist (sub and elem o), (active and elem h and neighbor elem n), 2.20
dist (active and elem o), (active and elem h and neighbor elem n), 2.20
hide label

# Hide unimportant atoms by mouse picking
cmd.select('lb',"(1HDU_carboxypeptidase_mono_H`1152)")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1151))) and not (((1HDU_carboxypeptidase_mono_H`1151)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1144))) and not (((1HDU_carboxypeptidase_mono_H`1144)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1153))) and not (((1HDU_carboxypeptidase_mono_H`1153)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1100))) and not (((1HDU_carboxypeptidase_mono_H`1100)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1099))) and not (((1HDU_carboxypeptidase_mono_H`1099)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1101))) and not (((1HDU_carboxypeptidase_mono_H`1101)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1091))) and not (((1HDU_carboxypeptidase_mono_H`1091)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`4204))) and not (((1HDU_carboxypeptidase_mono_H`4204)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`4203))) and not (((1HDU_carboxypeptidase_mono_H`4203)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`4205))) and not (((1HDU_carboxypeptidase_mono_H`4205)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`4196))) and not (((1HDU_carboxypeptidase_mono_H`4196)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`3053))) and not (((1HDU_carboxypeptidase_mono_H`3053)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`3043))) and not (((1HDU_carboxypeptidase_mono_H`3043)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`3052))) and not (((1HDU_carboxypeptidase_mono_H`3052)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`3051))) and not (((1HDU_carboxypeptidase_mono_H`3051)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`3057))) and not (((1HDU_carboxypeptidase_mono_H`3057)) in (lb)))")
cmd.select('lb',"( ((lb) or ((1HDU_carboxypeptidase_mono_H`1105))) and not (((1HDU_carboxypeptidase_mono_H`1105)) in (lb)))")
cmd.hide("everything","lb")
cmd.delete("lb")

# Zoom into the active site
set_view (\
    0.708307922,    0.458682060,   -0.536589086,\
    0.255396694,   -0.875151932,   -0.410964549,\
   -0.658090711,    0.154048845,   -0.737018764,\
    0.000052277,   -0.000042245,  -45.548389435,\
    6.132300854,    7.234283924,   -2.785414219,\
    2.500000000,  122.507408142,    0.000000000 )

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