Pymol结合界面绘制+结构比对+基本绘图命令

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Pymol绘图

选择氨基酸及周围构象

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fetch 2as5
remove solvent
# Select targer residue. chain, res, atom, as well.
sele res, chain M and resi 527
# 30 Angstrom
sele res_near30, chain M and resi 527 around 30
# 20 Angstrom
sele res_near, chain M and resi 527 around 20
# 取反
sele notnear, not res_near
# 透明度
set transparency, 0.3, res_near
residue structural context of 30 angstrom
residue structural context of 20 angstrom

结构比对

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super structure1 structure2
align structure1 structure2
pair_fit structure1///1-5/CA, structure2///1-5/CA

# superimpose protA residues 10-25 and 33-46 to protB residues 22-37 and 41-54:
pair_fit protA///10-25+33-46/CA, protB///22-37+41-54/CA
# superimpose ligA atoms C1, C2, and C4 to ligB atoms C8, C4, and C10, respectively:
pair_fit ligA////C1, ligB////C8, ligA////C2, ligB////C4, ligA////C3, ligB////C10
pair_fit
align or super

绘制复合体结合位点

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fetch 8eug
remove solvent

color pink

select chain3, chain 3
color yellow, chain3

select DNA,resn A+T+C+G
select bases,resn DA+DU+DC+DG+A+T+C+G
color white, bases

select aas, !bases
color pink, aas

select bs, chain 3 and resi 8+13+14+15+17+19+21+24+26+29+38+39+41
show sticks, bs
color cyan, bs
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fetch 3kfu
remove solvent

cartoon arrow,3kfu
show surface, 3kfu
select bases, resn A+T+C+G
color lime, bases

select aas, !bases
color pink, aas

select chainA, chain A
color yellow, chainA

select bs_3kfu, 3kfu and chain A and resi 24+25+26+27+28+29+30+31+33+44+68+70+72+76+91+93+95+98+102+103+104+107+111
color cyan, bs_3kfu
orient bs_3kfu
show sticks, bs_3kfu

Select atoms

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select aa1, only and resi 475
select aa2, 2x19 and resi 475 
select aa1_near, only and resi 475 around 5
select aa2_near, 2x19 and resi 475 around 5
select back_bone2, aa2_near and name c+o+n+ca

# calculate dihedral angles
phi_psi 2x19

Draw paper plot

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fetch 7lys

remove solvent
select dna, resn A+T+C+G+DT
select rna, resn DA+DU+DC+DG+U
select base, dna or rna
color tv_orange, base

select PI,chain A and resi 1-57
color lightblue, PI

select OBD,chain A and resi 57-73+196-363
color lightpink, OBD

select RecI, chain A and resi 73-196
color grey90,RecI

select RecII, chain A and resi 436-578
color grey50,RecII

select RuvC, chain A and resi 363-436+578-666+694-757
color limegreen, RuvC

select ZR, chain A and resi 666-694
color violet,ZR

color slate, rna
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fetch 5id6
remove solvent
select dna, resn A+T+C+G+DT
select rna, resn DA+DU+DC+DG+U
select base, dna or rna
color tv_orange, base
select protein, not base
color protein, lightpink


select H1,chain A and resi 1-292
color tv_yellow, H1

select H2,chain A and resi 292-515
color lightpink, H2

select OBD-L, chain A and resi 515-584+678-809
color palecyan, OBD-L

select LHD, chain A and resi 584-678
color violet,LHD

select RuvC, chain A and resi 809-858+890-1011+1138-1228
color gray90, RuvC

select HLH, chain A and resi 858-890
color tv_green,HLH

select UK, chain A and resi 1011-1138
color marine,UK
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bg_color white
fetch 6vpc
remove solvent
select dna, resn A+T+C+G+DT
select rna, resn DA+DU+DC+DG+U
select base, dna or rna
color tv_orange, base
select protein, not base
color protein, lightpink

show cartoon
show surface
hide lines
set transparency,0.8
set surface_quality,1
select Cas, chain B
select RuvC,Cas and resi 201-256+918-980+1106-1299
select REC,Cas and resi 294-918
select NHN, Cas and resi 980-1106
select PI, Cas and resi 1299-1568
select link, Cas and not RuvC and not REC and not NHN and not PI

select sgRNA, chain A
select TS, chain C
select NTS, chain D

color deeppurple, sgRNA
color forest,TS
color marine, NTS

color gray90, link
color cyan, RuvC
color gray90, REC
color tv_orange, NHN
color tv_yellow, PI

select Tad1, chain E
select Tad2, chain F
color tv_red,Tad1
color salmon, Tad2


set cartoon_fancy_helices, 1
set cartoon_smooth_loops, 1
set cartoon_dumbbell_width, 0.1

set cartoon_ring_mode, 6
set cartoon_ring_transparency 0.50000
set cartoon_tube_radius, 0.75
cartoon rectangle, base

set ray_trace_mode, 3
set ray_shadows, off
set antialias, 2


png ./myimage.png, width=12cm, dpi=300, ray=1