# PyMOL script for lysozyme_NAG3
# jdc 2014_10_25

# lzm-NAG3 complex
load 1HEW.pdb, lzm

select polypep, resi 1-129
select NAG, resn NAG
select E35, resi 35
select D52, resi 52
select bind, resi 37 or resi 62 or resi 63 or resi 101 or resi 108 or resi 114
select mc_ints, resi 107 or resi 109 or resi 57 or resi 59 or resi 34 or (resi 35 and (name c+o))

select loops, resi 4 or resi 16-24 or resi 36-37 or resi 41 or resi 47-49 or resi 55-56 or resi 61-79 or resi 85-88 or resi 99-108 or resi 114-129

select water, resn HOH
disable water

hide everything

set stick_radius=0.2
set sphere_scale=0.2

util.cbab polypep
util.cbay NAG

show sticks, NAG
show sticks, E35 & not(name n+c+o)
show sticks, D52 & not(name n+c+o)

set cartoon_transparency, 0.5
cartoon dumbbell
set cartoon_highlight_color, grey50
show cartoon, polypep

# if you like a view in PyMOL, use the "Get View" button
# (right side of upper Tk window), which outputs a view
# matrix like the following to paste in to your script:
set_view (\
0.645015121, 0.532275796, 0.548300564,\
-0.618126571, -0.058452200, 0.783899903,\
0.449303359, -0.844547451, 0.291313231,\
0.000046641, 0.000088371, -96.938911438,\
-0.932261467, 20.096065521, 22.753320694,\
70.098320007, 123.774345398, -20.000000000 )