The following script was used:
#
Y2R_superpose_active_inactive.pml
# ---------------------------------
reinitialize
# load structures
# ---------------
fetch 7yon, active
fetch 7ddz, inactive
align model inactive and name CA, model active and name CA
# create objects
# --------------
create Y2a, active and chain R
create YY, active and chain L
create Y2i, inactive and chain A and resi 1-343 ;# omit ICL3 fusion
#create Galpha, chain A
#create Gbeta, chain B
#create Ggamma, chain G
# general definitions and graphics
# --------------------------------
set hash_max, 100
set bg_rgb, white
set depth_cue, on
set fog, 1.0
set fog_start, 0.6
set orthoscopic, on
clip slab, 100
set opaque_background, on
set ray_shadows, off
hide everything
#@D:\pymol_examples\def_colours.pml
# fold cartoon
# ------------
dss
set cartoon_fancy_helices, on
# set cartoon_highlight_color, white
#set cartoon_transparency, 0.7, resi 233-249 ;# this is to provide a
better view for the helix 6 movement in ray tracing mode
show cartoon, Y*
#color orange, YY
set cartoon_color, grey30
#color deepblue, Gbeta
#color aquamarine, Ggamma
#set cartoon_color, paleblue, receptor
#util.chainbow()
# molecular surface
# -----------------
#create msurface, receptor
#hide all, msurface
show surface, Y*
set transparency, 0.5
set surface_color, gold
# viewpoint
# ---------
#orient Y2a ; # this orients the 7TM domain along its principal axis
such that the helices are parallel to x (longest dimension)
#turn z, 90 ; # rotate 7TM such that helices are vertical
#turn y, -90 ; # rotate around vertical axis
#zoom
# ***********PASTE VIEW MATRIX HERE ************
viewport 400,600
# morph
# -----
util.performance(0)
morph morph01, Y2i, Y2a
mset 1 x30
madd 1-30
madd 30 x30
madd 30-1
mplay
set_view (\
0.802717209,
0.122951634, 0.583526075,\
-0.466776222,
-0.479430526, 0.743127942,\
0.371141285,
-0.868901372, -0.327459961,\
-0.001843914, 0.006589606,
-238.264129639,\
167.780471802, 171.087127686, 142.510864258,\
198.309188843, 277.988677979,
20.000000000 )
# for final raytracing:
# util.performance(0)
# ray/draw 500, 900
# png 4eiy_protein.png