#-------------------------------------------------------------------------------
# cmura@virginia.edu, 12may2010
# NOTES:
# - See also http://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels
#-------------------------------------------------------------------------------

fetch 2ajr, async=0
cmd.copy('2ajr_copy','2ajr')

bg_color white
hide everything, all

# Want residue range [63,79] to be semi-transparent:
#select myFrontHelix, (/2ajr//B/63:79)
select myFrontHelix, (///B/63:79)

util.color_chains("2ajr or 2ajr_copy")
set cartoon_transparency, 0.6, 2ajr_copy

show cartoon, all
set cartoon_fancy_helices, 1
set cartoon_highlight_color, grey

select forSpheres, (2ajr & c;B & i;11)
show spheres, forSpheres
util.cbaw("forSpheres")

# The key step:
cartoon skip, (2ajr_copy and not myFrontHelix)
cartoon skip, (2ajr and myFrontHelix)

deselect
set_view (\
     0.812660635,   -0.580136895,   -0.054995447,\
     0.395680070,    0.618619382,   -0.678784192,\
     0.427808881,    0.529860556,    0.732275069,\
     0.000000000,    0.000000000, -201.032897949,\
    52.504463196,   11.987812042,  122.190872192,\
   152.703445435,  249.362319946,  -20.000000000 )

ray
png cartoonTrans.png

#quit