fetch 3uex, struct, async=0
remove solvent
# set the B-factors nice and high for smoothness
alter all, b=10
alter all, q=1
# 3.5 A map resolution
set gaussian_resolution, 3.5
# new gaussian map w/resolution=0.5 Ang
# on just the main chain
map_new map, gaussian, 0.5, n. C+O+N+CA, 5
# create a surface from the map
isosurface surf, map, 3.0
# color the protein by number
spectrum count, rainbow, struct
# now color the map based on the underlying protein
cmd.ramp_new("ramp", "struct", [0,10,10], [-1, -1, 0])
# set the surface color
cmd.set("surface_color", "ramp", "surf")
# hide the ramp and lines
disable ramp
hide lines
bg grey
# soften out the image
set light_count,8
set spec_count,1
set shininess, 10
set specular, 0.075
set ambient,0
set direct,0
set reflect, 0.85
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 4
unset depth_cue
# ray trace the image
orient
ray
image.png
fetch 1eaz, async=0
extract oo, org
hide everything, solvent
set field_of_view, 50
preset.ball_and_stick("oo")
set_bond stick_color, 0xffff44, oo
set_bond stick_transparency, 0.35, oo
color grey, oo and e. C
set valence, 1, oo
ramp_new pRamp, oo, selection=poly, range=[5,30], color=rainbow
set surface_color, pRamp, poly
show spheres, poly
color white, poly
color grey30, poly and e. C
set sphere_scale, 0.99, poly
set ray_transparency_contrast, 0.20
set ray_transparency_oblique, 1.0
set ray_transparency_oblique_power, 20
show surface, poly
set surface_quality, 2
set light_count, 5
set ambient_occlusion_mode, 1
set ambient_occlusion_scale, 50
set ambient, 0.40
set transparency, 0.50
disable pRamp
set spec_power, 1200
set spec_reflect, 0.20
set ray_opaque_background, 0
set ray_shadow, 0
ray
image.png
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