pymol做图简单教程

1、1.2.3.在里面找出 ligand,点 sclc 的 A (action)/rename将对接好的ligand和蛋白merge（好像每次只能用一个ligand和一个蛋白，否则pymol里会 把几个ligand当作一个Merge 后 export structure:,存成 pdb 格式在pymol中打开.pdb2J502国 EH9Rename这个ligand,这里命名为lig5.6.选 all,H (hide)evcrthing选 lig, S(show)sticks(Llg-2> 2J5027.2j50（就是那个蛋白）S/cartoon8.在后面的color调整颜色，这里ligand

2、选by elementASAtoms| Color：| HHQS.一CUNOS._ CH OS CH 0S._ CH OS CH OS 1"fby chain(by ss.pectr nn卜auto12j50 选 whitecyansoranges tintsGrayswhite gray90 graySO gray/O gray60grays9.下面显示氢键，点击 2j50 的 Action,选择 find/polar contacks/to other atoms in objuct,氢键就出 来了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.然后再找氢键作用的残基，可以在上面直接点选，但最好找出氨基酸代码来选取（因为这里面点不灌）LALHk/LFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILgYEPLGTVYRELQKRunamu它们，以便以后好找，这里ru

5、namu为rus, show它们为linu, color为by ulumunt11 .再选 display,将 background 改成 white12.然后分别点选这几个心（因为颜色不同,所以很容易找出来），右键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出来后，还可以调整它们的位置点一下左囱vicving,就变成了右图的editing,这时就可 以按住Ctrl键拖动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 .大体已经完成了，再进行一些修饰G LU-211GLU-211Setting/ mmsparency/cart（）（）n/ 50% 蛋白的透明度Sctring/labcl/sizc 18调节字体的大小Setrin

8、g/edit allcartoon的颜色改回白色（在filter里输cartoon可以快点找出来，改完后按回车） 或者输入命令 PyrrK）l>sci cart（）（）n_cok）r while在改氢键的线型，在dash gap length width进行调整把虚线改好看点Stick也可以改细点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.电子密度1）首先，登陆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) 选 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）下载后解压，重命a为*.m叩.ccp42j 50. m铀.ccp45)在 pymol 里打开，在打开的.map,action/mush,color/bluu6)选中 lig,在 PyMOL 输入 isomush map,2j50.map>2.0,sclc.carvc=l .67）这样就从原来的map S iso出lig周围的蛋白的电子密度，把2j50.