Pymol高级作图技巧汇总
一、设置背景为透明
在Pymol主菜单中选择setting->Edit All...,然后从搜索框中查找opaque_background, 将其设置为off
设置螺旋的宽度:
setting... -> EditALL
cartoon_dumbbell_length 1.8 cartoon_oval_length 1.65
修改折叠的宽度:
cartoon_rect_length 1.60
修改distance的颜色:
1> 首先,将distance 设置成为你想要改变成的颜色,例如 color black dis1 (dis1这个名称为你自己命名的distance的名称)
2> 在setting...-> Edit All中设置label的颜色,在Edit All中查找参数 label_color , 将此参数设置成和你要改变distance相同的颜色,如black
二、Pymol中自己挑选的几种漂亮的颜色设置及着色
set_color color1, [186,182,217]
set_color color2, [233,195,153]
set_color color3, [141,215,247]
set_color color4, [206,155,198]
set_color color5, [251,187,62]
set_color color6,[245,157,158]
set_color color7, [133,188,135]
三、使用命令标记两个原子之间的距离
dist dist_name, atom1, atom2 (atom1和atom2可以用select 命令进行定义)
示例(APN3):
set_color color1, [206,155,198]
set_color color2, [233,195,153]
set_color color3, [141,215,247]
set_color color4, [146,146,197]
set_color color5, [251,187,62]
set_color color6, [114,192,101]
set_color color7, [162,209,157]
select rdomain1, A/51-272/*
select rdomain2, A/273-521/*
select rdomain3, A/522-630/*
select rdomain4, A/631-1024/*
color color1,rdomain1
color color2,rdomain2
color color3, rdomain3
color color4,rdomain4
select ldomain1, B/32-253/*
select ldomain2, B/254-462/*
select ldomain3, B/463-611/*
color color5, ldomain1
color color6, ldomain2
color color7, ldomain3
set_color color_o, [238,71,71]
set_color color_n, [30,30,151]
set_color color_s, [201,173,56]
select receptor_res_c, A/121+128+142+175+182+86+119+118+116+176+126/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select receptor_res_o, A/121+128+142+175+182+86+119+118+116+176+126/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/121+128+142+175+182+86+119+118+116+176+126/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/121+128+142+175+182+86+119+118+116+176+126/SD
select ligand_res_c, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/SD
color color_o, receptor_res_o
color colo
set_color color2, [233,195,153]
set_color color3, [141,215,247]
set_color color4, [146,146,197]
set_color color5, [251,187,62]
set_color color6, [114,192,101]
set_color color7, [162,209,157]
select rdomain1, A/51-272/*
select rdomain2, A/273-521/*
select rdomain3, A/522-630/*
select rdomain4, A/631-1024/*
color color1,rdomain1
color color2,rdomain2
color color3, rdomain3
color color4,rdomain4
select ldomain1, B/32-253/*
select ldomain2, B/254-462/*
select ldomain3, B/463-611/*
color color5, ldomain1
color color6, ldomain2
color color7, ldomain3
set_color color_o, [238,71,71]
set_color color_n, [30,30,151]
set_color color_s, [201,173,56]
select receptor_res_c, A/121+128+142+175+182+86+119+118+116+176+126/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select receptor_res_o, A/121+128+142+175+182+86+119+118+116+176+126/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/121+128+142+175+182+86+119+118+116+176+126/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/121+128+142+175+182+86+119+118+116+176+126/SD
select ligand_res_c, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/SD
color color_o, receptor_res_o
color colo