Sometimes it can be difficult to show buried protein-ligand interactions.
fetch 3ert, async=0 select lig, 3ert and organic, enable=0 hide 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 ray