pymol做圖簡(jiǎn)單教程

1、1.2.3.在里面找出 ligand,點(diǎn) sclc 的 A (action)/rename將對(duì)接好的ligand和蛋白merge（好像每次只能用一個(gè)ligand和一個(gè)蛋白，否則pymol里會(huì) 把幾個(gè)ligand當(dāng)作一個(gè)Merge 后 export structure:,存成 pdb 格式在pymol中打開.pdb2J502國(guó) EH9Rename這個(gè)ligand,這里命名為lig5.6.選 all,H (hide)evcrthing選 lig, S(show)sticks(Llg-2> 2J5027.2j50（就是那個(gè)蛋白）S/cartoon8.在后面的color調(diào)整顏色，這里ligand

2、選by elementASAtoms| Color：| HHQS.一CUNOS._ CH OS CH 0S._ CH OS CH OS 1"fby chain(by ss.pectr nn卜auto12j50 選 whitecyansoranges tintsGrayswhite gray90 graySO gray/O gray60grays9.下面顯示氫鍵，點(diǎn)擊 2j50 的 Action,選擇 find/polar contacks/to other atoms in objuct,氫鍵就出 來了2J502Action；lig-2_pozoomorientcenterorigi

3、n drag matrixreset matrixdrag coordinatesclean( Polar Contacts；Find；within selection involving side chains inuoluing solvent excluding solvent excluding main chain excluding intra-main chain Just intra-side chain J List intra-main chainfindialign generateassign sec struc.rename object duplicate obje

4、ct delete objecthydrogens remove watersstatei maskingto other atoms in objectto others excluding solvent to any atomsto any excluding solventsequencemovement,compute10.然后再找氫鍵作用的殘基，可以在上面直接點(diǎn)選，但最好找出氨基酸代碼來選取（因?yàn)檫@里面點(diǎn)不灌）LALHk/LFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILgYEPLGTVYRELQKRunamu它們，以便以后好找，這里ru

5、namu為rus, show它們?yōu)閘inu, color為by ulumunt11 .再選 display,將 background 改成 white12.然后分別點(diǎn)選這幾個(gè)心（因?yàn)轭伾煌?所以很容易找出來），右鍵labcl/rcsiducs156sei e6 171 176 131 186| disable 'colorshowhideLabel ：(label 1clearzoomresiduesorientchainscentersegmentsoriginatom namedragelement symbolcleanresidue narerV CiIT. C 1 1 Ur

6、esidue i denti Fi er13.1abcl出來后，還可以調(diào)整它們的位置點(diǎn)一下左囪vicving,就變成了右圖的editing,這時(shí)就可 以按住Ctrl鍵拖動(dòng)label的位置了Mou.se Mode 3-Bu.tton Viewing：ButtonsLMRWheel& KeysRotaMoveMovZSlabShFt+ Box-BoxClipMovSCtrl+ /-PkAtPklMuS乙CtShSei eOrigClipMovZSnglClk+ /-CentMenu.DblClkMenuPkAtSelecting Residues>State1/1Mouse Mode

7、 3-Button EditingButtons LMRWheel& KeysRotaMoveMovZSlabShftRotOMovOMvOZMovSCtrlMov APkTBMvSZCtShMvAZOrigClipMovZSnglClkPkAtCentMenuDblClkMov ADrgMPkTBPickingAtoms (anc1 Jolnts>State1/112 .大體已經(jīng)完成了，再進(jìn)行一些修飾G LU-211GLU-211Setting/ mmsparency/cart（）（）n/ 50% 蛋白的透明度Sctring/labcl/sizc 18調(diào)節(jié)字體的大小Setrin

8、g/edit allcartoon的顏色改回白色（在filter里輸cartoon可以快點(diǎn)找出來，改完后按回車） 或者輸入命令 PyrrK）l>sci cart（）（）n_cok）r while在改氫鍵的線型，在dash gap length width進(jìn)行調(diào)整把虛線改好看點(diǎn)Stick也可以改細(xì)點(diǎn)line_stick_helperonroving -sticks6.00000stick.balloffstick-ball jcolordefeultstick.balLratio1.00000stick-colordefaultstick.fixed.radiusoffstick_h_sc

9、ale0.40000stiGk._nub0.70000stick_overlap0.20000stick_quality8stick_radius0.2000sti ck_tr ansparency0.00000stick_valence_scale1.0000013.電子密度1）首先，登陸http:uds.bmc.uu.su/uds/搜索你的蛋白Welcome to the Electron Density Server at Uppsala University2) download mapsveu dimensions: aDownloadCoordinatesMapsStatistic

10、sAll files (tar.£z)7czt£Number of reflections: 1 (Correlation coefficient Fo C and Fc :3) 選 ccp4 格式,genuratu mapElectron-density map generation for 2j50fomiat: o Type mFo-DFcjJ Generate map |o ICCP4CNS(Note: this, may take a eZD = or many minutes, depending on the size of your map.)4）下載后解壓，重命a為*.m叩.ccp42j 50. m鈾.ccp45)在 pymol 里打開，在打開的.map,action/mush,color/bluu6)選中 lig,在 PyMOL 輸入 isomush map,2j50.map>2.0,sclc.carvc=l .67）這樣就從原來的map S iso出lig周圍的蛋白的電子密度，把2j50.