Pymol高级作图技巧汇总
来源：互联网 发布：8080端口怎么关闭 编辑：程序博客网 时间：2024/05/16 13:46
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 color_n, receptor_res_n
color color_s, receptor_res_s
color color_o, ligand_res_o
color color_n, ligand_res_n
color color_s, ligand_res_s
select receptor_res, A/121+128+142+175+182+86+119+118+116+176+126/*
select ligand_res, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/*
show sticks,receptor_res
show sticks,ligand_res
distance dis1, A/121/OG1 , B/293/O
distance dis2, A/121/OG1 , B/293/OG
distance dis3, A/128/N , B/482/O
distance dis4, A/142/OH , B/306/OH
distance dis5, A/175/ND2 , B/440/O
distance dis6, A/175/ND2 , B/442/OD1
distance dis7, A/175/ND2 , B/443/OG
distance dis8, A/175/ND2 , B/444/OG
distance dis9, A/182/NZ , B/443/O
distance dis10, A/182/NZ , B/444/OG
distance dis11, A/86/OD2 , B/281/N
distance dis12, A/121/OG1 , B/293/N
distance dis13, A/121/OG1 , B/293/OG
distance dis14, A/142/OH , B/306/OH
distance dis15, A/119/O , B/338/OH
distance dis16, A/118/OD1 , B/339/N
distance dis17, A/116/OD2 , B/341/N
distance dis18, A/116/O , B/437/NH1
distance dis19, A/176/OD1 , B/442/ND2
distance dis20, A/175/OD1 , B/444/OG
distance dis21, A/126/O , B/484/N
distance dis22, A/126/O , B/485/N
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 color_n, receptor_res_n
color color_s, receptor_res_s
color color_o, ligand_res_o
color color_n, ligand_res_n
color color_s, ligand_res_s
select receptor_res, A/121+128+142+175+182+86+119+118+116+176+126/*
select ligand_res, B/293+482+306+440+442+443+444+281+338+339+341+437+484+485/*
show sticks,receptor_res
show sticks,ligand_res
distance dis1, A/121/OG1 , B/293/O
distance dis2, A/121/OG1 , B/293/OG
distance dis3, A/128/N , B/482/O
distance dis4, A/142/OH , B/306/OH
distance dis5, A/175/ND2 , B/440/O
distance dis6, A/175/ND2 , B/442/OD1
distance dis7, A/175/ND2 , B/443/OG
distance dis8, A/175/ND2 , B/444/OG
distance dis9, A/182/NZ , B/443/O
distance dis10, A/182/NZ , B/444/OG
distance dis11, A/86/OD2 , B/281/N
distance dis12, A/121/OG1 , B/293/N
distance dis13, A/121/OG1 , B/293/OG
distance dis14, A/142/OH , B/306/OH
distance dis15, A/119/O , B/338/OH
distance dis16, A/118/OD1 , B/339/N
distance dis17, A/116/OD2 , B/341/N
distance dis18, A/116/O , B/437/NH1
distance dis19, A/176/OD1 , B/442/ND2
distance dis20, A/175/OD1 , B/444/OG
distance dis21, A/126/O , B/484/N
distance dis22, A/126/O , B/485/N
APN1
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, [167,70,151]
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, [167,70,151]
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]
select rdomain1, A/51-260/*
select rdomain2, A/261-521/*
select rdomain3, A/522-613/*
select rdomain4, A/614-865/*
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/*
select rdomain2, A/261-521/*
select rdomain3, A/522-613/*
select rdomain4, A/614-865/*
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
color color6, ldomain2
color color7, ldomain3
select receptor_res, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/*
select ligand_res, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/*
select receptor_res_c, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select receptor_res_o, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/SD
select ligand_res_c, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/SD
select receptor_res_o, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/103+122+124+162+169+173+105+104+102+120+94+173+323+794/SD
select ligand_res_c, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/595+593+510+509+442+437+341+337+320+306+482+485+435+339+335+334/SD
set_color color_o, [238,71,71]
set_color color_n, [30,30,151]
set_color color_s, [201,173,56]
set_color color_n, [30,30,151]
set_color color_s, [201,173,56]
color color_o, receptor_res_o
color color_n, receptor_res_n
color color_s, receptor_res_s
color color_o, ligand_res_o
color color_n, ligand_res_n
color color_s, ligand_res_s
color color_n, receptor_res_n
color color_s, receptor_res_s
color color_o, ligand_res_o
color color_n, ligand_res_n
color color_s, ligand_res_s
distance dis1 ,A/103/N ,B/334/O
distance dis2 ,A/103/OG1 ,B/320/OE1
distance dis3 ,A/103/OG1 ,B/335/O
distance dis4 ,A/122/N ,B/339/O
distance dis5 ,A/124/ND2 ,B/435/O
distance dis6 ,A/162/OG1 ,B/482/O
distance dis7 ,A/162/OG1 ,B/485/O
distance dis8 ,A/169/NH1 ,B/482/O
distance dis9 ,A/169/NH2 ,B/482/O
distance dis10 ,A/173/N ,B/509/OE1
distance dis11 ,A/105/O ,B/306/OH
distance dis12 ,A/104/O ,B/320/NE2
distance dis13 ,A/105/OG1 ,B/320/NE2
distance dis14 ,A/102/O ,B/337/N
distance dis15 ,A/120/O ,B/341/N
distance dis16 ,A/122/O ,B/437/NH1
distance dis17 ,A/122/O ,B/437/NH2
distance dis18 ,A/94/OE1 ,B/442/ND2
distance dis19 ,A/94/OE2 ,B/442/ND2
distance dis20 ,A/173/O ,B/509/NE2
distance dis21 ,A/323/OD1 ,B/510/ND2
distance dis22 ,A/794/OD2 ,B/593/OG
distance dis23 ,A/794/OD1 ,B/595/OG1
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]
select rdomain1, A/51-261/*
select rdomain2, A/262-521/*
select rdomain3, A/522-613/*
select rdomain4, A/614-959/*
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/*
select rdomain2, A/262-521/*
select rdomain3, A/522-613/*
select rdomain4, A/614-959/*
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
color color6, ldomain2
color color7, ldomain3
select receptor_res, A/399+461+396/*
select ligand_res, B/503+504+510+509/*
select ligand_res, B/503+504+510+509/*
APN5
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, [167,70,151]
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, [167,70,151]
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]
select rdomain1, A/51-259/*
select rdomain2, A/260-523/*
select rdomain3, A/524-615/*
select rdomain4, A/616-959/*
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/*
select rdomain2, A/260-523/*
select rdomain3, A/524-615/*
select rdomain4, A/616-959/*
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
color color6, ldomain2
color color7, ldomain3
select receptor_res, A/399+403+396+408+467/*
select ligand_res, B/503+504+510+590/*
select ligand_res, B/503+504+510+590/*
select receptor_res_c, A/399+403+396+408+467/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select receptor_res_o, A/399+403+396+408+467/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/399+403+396+408+467/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/399+403+396+408+467/SD
select ligand_res_c, B/503+504+510+590/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/503+504+510+590/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/503+504+510+590/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/503+504+510+590/SD
select receptor_res_o, A/399+403+396+408+467/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/399+403+396+408+467/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/399+403+396+408+467/SD
select ligand_res_c, B/503+504+510+590/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/503+504+510+590/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/503+504+510+590/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/503+504+510+590/SD
set_color color_o, [238,71,71]
set_color color_n, [30,30,151]
set_color color_s, [201,173,56]
set_color color_n, [30,30,151]
set_color color_s, [201,173,56]
color color_o, receptor_res_o
color color_n, receptor_res_n
color color_s, receptor_res_s
color color_o, ligand_res_o
color color_n, ligand_res_n
color color_s, ligand_res_s
color color_n, receptor_res_n
color color_s, receptor_res_s
color color_o, ligand_res_o
color color_n, ligand_res_n
color color_s, ligand_res_s
distance dis1 ,A/399/OG ,B/503/O
distance dis2 ,A/399/OG ,B/504/O
distance dis3 ,A/403/O ,B/503/OG
distance dis4 ,A/396/O ,B/510/ND2
distance dis5 ,A/408/OD2 ,B/510/ND2
distance dis6 ,A/467/OE2 ,B/590/NH2
distance dis2 ,A/399/OG ,B/504/O
distance dis3 ,A/403/O ,B/503/OG
distance dis4 ,A/396/O ,B/510/ND2
distance dis5 ,A/408/OD2 ,B/510/ND2
distance dis6 ,A/467/OE2 ,B/590/NH2
APN6
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, [167,70,151]
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, [167,70,151]
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]
select rdomain1, A/51-261/*
select rdomain2, A/262-521/*
select rdomain3, A/522-613/*
select rdomain4, A/614-959/*
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/*
select rdomain2, A/262-521/*
select rdomain3, A/522-613/*
select rdomain4, A/614-959/*
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
color color6, ldomain2
color color7, ldomain3
select receptor_res, A/399+461+396/*
select ligand_res, B/503+504+510+509/*
select ligand_res, B/503+504+510+509/*
select receptor_res_c, A/399+461+396/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select receptor_res_o, A/399+461+396/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/399+461+396/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/399+461+396/SD
select ligand_res_c, B/503+504+510+509/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/503+504+510+509/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/503+504+510+509/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/503+504+510+509/SD
select receptor_res_o, A/399+461+396/O+OG1+OG2+OD1+OD2+OH+OG
select receptor_res_n, A/399+461+396/N+ND1+ND2+NZ+NE+NH1+NH2
select receptor_res_s, A/399+461+396/SD
select ligand_res_c, B/503+504+510+509/C+CA+CB+CG+CG1+CG2+CE1+CE2+CD1+CD2+CZ+CE+CD
select ligand_res_o, B/503+504+510+509/O+OG1+OG2+OD1+OD2+OH+OG
select ligand_res_n, B/503+504+510+509/N+ND1+ND2+NZ+NE+NH1+NH2
select ligand_res_s, B/503+504+510+509/SD
distance dis1 ,A/399/OG ,B/503/O
distance dis2 ,A/399/OG ,B/504/O
distance dis3 ,A/461/O ,B/509/NE2
distance dis4 ,A/396/O ,B/510/ND2
0 0
- Pymol高级作图技巧汇总
- pymol 知道多少？pymol技巧汇总
- Pymol（1.8.6）作图技巧之创建质心
- MATLAB作图技巧汇总
- Pymol（1.8.6）作图技巧之cartoon和surface镶嵌模型
- CSS 高级技巧汇总
- JS高级技巧汇总
- css高级技巧汇总
- R作图技巧
- 一些作图技巧
- nc.exe高级技巧应用汇总
- CSS在使用中的高级技巧汇总
- 12 个 CSS 高级技巧汇总
- 12 个 CSS 高级技巧汇总
- 12 个 CSS 高级技巧汇总
- 12个css高级技巧汇总
- 20 个 CSS 高级技巧汇总
- 12 个 CSS 高级技巧汇总
- js 将json字符串转换为json对象的方法解析
- markdown文件转pdf
- 深入理解Android之设备加密Device Encryption
- ViewPager与百度地图冲突的纯净解决方案
- Python图表绘制：matplotlib绘图库入门
- Pymol高级作图技巧汇总
- java创建线程implement runnable 和 extends thread 比较
- JS定时刷新页面及跳转页面
- 从源码看invalidate和requestLayout的区别
- Java集合框架List，Map，Set等全面介绍+vector VS ArrayList
- 百度地图图片不显示
- UE Bearer Capability 1
- UE4官方文档_Light Propagation Volumes_LPV方案
- LTE系统信息（3）-系统信息变更
