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

 

select N1_6A, N1_trim & resid 73+74+75+76+77+78+79+82+83+84+86+87+88+177+181+182+183+184+185+204+205+208+211+212+215+269+271+272+273+275+276+277+278+279+280+281+282+284+341+342+343+345+346+458+459+460+461+462

 

绘制底物结合口袋

remove solvent 去除溶剂分子

选中部分，Action下拉菜单， extract object 提取选中的部分

zoom (), animate 1 放大选中部分

bg_color white 设置背景颜色为白色（或其他black or gray）

set cartoon_transparency, 0.8 调整cartoon(或其他surface......)的透明度

 

select (object) around (distance) 选择距某物体xÅ之内的物体

select active, byres all within (distance) of (object)选择距某物体xÅ之内的物体

（不太清楚两者区别，自己用的后一种）

将选中的活性口袋内的氨基酸提取，Action下拉菜单，generate，vacuum electrostatics，protein contact potential