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Carving Surfaces

Sometimes it can be difficult to show buried protein-ligand interactions.

fetch 3ert, async=0
select lig, 3ert and organic, enable=0
show sticks, lig,
show surface, 3ert within 5 of lig
set two_sided_lighting
orient lig
clip slab, 7
clip move, -2
show lines, byres (3ert within 5 of lig)

clip slab, 10

Surface carving can limit visible portions of the surface using a geometric cutoff based on proximity to a translated copy of the ligand.

# create a copy of the ligand

create lig_copy, organic, zoom=0

# color it cyan

color cyan, lig_copy

# translate it away from the camera

translate [0,0,-3], lig_copy

# now "carve" the surface to only show 
set surface_carve_selection, lig_copy
set surface_carve_cutoff, 3

Now a figure can be generated with only half of the binding site surface shown.

# hide the extra copy of the ligand

disable lig_copy

# change the colors

set surface_color, white
color yellow, lig and elem c
set line_width, 3

# ray trace for shadows


figure/carving_surfaces.txt · Last modified: 2013/08/19 21:00 (external edit)