pymol常用操作

1、Con trol-Shift-Middle-Click確定旋轉(zhuǎn)中心右鍵+中間鍵拖動(dòng)分子show/hide lines顯示/隱藏全部show/hide sticks 棒狀顯示Cartoon:主鏈，mesh：網(wǎng)孔結(jié)構(gòu)，spheres：球狀結(jié)構(gòu)；ribbon :線條；surface:表面結(jié)構(gòu)基本命令（也可使用鼠標(biāo)操作，但不如命令來得簡單）pwd# show curre nt directorydir# list file in the curre nt directorycd directory #cha nge directoryload xxx#注意要打上擴(kuò)展名，例如 1LMK.pdb，否則會(huì)e

2、rrorcreat n ame, (select ion) #n ame=object to creat, selecti on=atom to in clude in the new object, 非常實(shí)用的功能Mani pulati ng object: show represe ntati on, (select ion)hide represe ntati on, (select ion)#the available represe ntati ons are:(前面是個(gè)人比較常用的)lin es, spheres, ribb on, cartoon, sticks, surface

3、, / mesh, dots, labels, exte nt 例如：stick mol1 & resi 100# mol1為顯示在 pymol右邊的分子名稱Turn an object on and off:(這個(gè)直接用鼠標(biāo)就 ok 了)en able/disable, object- name #tur n on/off all represe ntati on縮寫n.<>例子:r.<>i.<>c.<>e.<>show cartoo n, (n. 1LDK/)Basic atom select ions: n ame &l

4、t;atom n ames> resn< residue types> resi<residue nu mber> cha in <cha in ID> elem<eleme nt symbol>Select ion algebra:就是怎么選擇交集是 and、&，例如 1LDK and chain A and i. 1-103 并集是or/|,補(bǔ)集是not/!Change your point of view:zoom, (select ion) #fit the select ion to scree norie nt, (se

5、lecti on)#alig n molecular axiscen ter, (select ion) # size not cha ngedturn axis, an gle #rotate cameramove axis, dista nee #tra nslate cameraAlign （個(gè)人認(rèn)為最重要的功能）： alig n (source), (target) #the source object will be moved and rotated to fit the target object例如： alig n (prot1 and cha in A), (prot2 an

6、d chain B)按整條鏈疊合alig n mol1 & resi N1, mol2 & resi N2按某一個(gè)殘基疊合align mol1 & resi N1-N2 & name n+ca+c+o , mol2 & resi N3-N4 & name n+ca+c+o 按 某段殘基的主鏈進(jìn)行疊合在align的過程中會(huì)產(chǎn)生一個(gè)root mean square deviation (RMSD),這個(gè)值可在一定程度上衡量alignment 的效果。Set con trol (可以通過這個(gè)命令來調(diào)整所有參數(shù)的值，可惜沒有什么詳細(xì)的介紹)例女口 set sphere_scale, 0.5, (n. Fe) #decrease Fe atom size to 0.5set bg_rgb, 1,1,1 #set backgro und as whiteset ribb on _sampli ng, 1Measureme nt (又一個(gè)十分重要的功能，可以真正挖掘結(jié)構(gòu)的意義)dist#測量兩個(gè)原子之間的距離，c