PYMOL显示底物周围surface

load $TUT/1hpv.pdb, tmp

extract lig, organic

extract prot, polymer

delete tmp

set surface_carve_cutoff, 5

set surface_carve_selection, lig

set surface_carve_normal_cutoff, -0.5

set surface_cavity_mode, 1

set surface_smooth_edges, 1

set surface_proximity, 1

set transparency, 0.6

set ray_shadows, 0

set two_sided_lighting

show surface, prot within 5 of lig

show sticks, lig

orient lig

set surface_color, limegreen

set surface_type, 2 # mesh

png overview.png, 20cm, 18cm, dpi=300, ray=1