我的Pymol部分常用命令.docx

基本命令（也可使用鼠标操作，但不如命令来得简单）pwd # show current directorydir # list file in the current directorycd directory #change directoryload xxx #注意要打上扩展名，例如1LMK.pdb，否则会errorcreat name, (selection) #name=object to creat, selection=atom to include in the new object, 非常实用的功能Manipulating object:show representation, (selection)hide representation, (selection)#the available representations are: (前面是个人比较常用的)lines, spheres, ribbon, cartoon, sticks, surface, / mesh, dots, labels, extent例如： stick mol1 & resi 100 # mol1为显示在pymol右边的分子名称Turn an object on and off:(这个直接用鼠标就ok了)enable/disable, object-name #turn on/off all representationBasic atom selections:name 缩写 n. 例子： show cartoon, (n. 1LDK/)resn r. resi i.chain c.elem e.Selection algebra: 就是怎么选择交集是and、&，例如 1LDK and chain A and i. 1-103并集是or/|，补集是not/!Change your point of view:zoom, (selection) #fit the selection to screenorient, (selection) #align molecular axiscenter, (selection) # size not changedturn axis, angle #rotate cameramove axis, distance #translate cameraAlign (个人认为最重要的功能)：align (source), (target) #the source object will be moved and rotated to fit the target object例如： align (prot1 and chain A), (prot2 and chain B) 按整条链叠合 align mol1 & resi N1, mol2 & resi N2 按某一个残基叠合 align mol1 & resi N1-N2 & name n+ca+c+o，mol2 & resi N3-N4 & name n+ca+c+o 按某段残基的主链进行叠合在align的过程中会产生一个root mean square deviation (RMSD),这个值可在一定程度上衡量alignment的效果。Set control (可以通过这个命令来调整所有参数的值，可惜没有什么详细的介绍)例如 set sphere_scale, 0.5, (n. Fe) #decrease Fe atom size to 0.5set bg_rgb, 1,1,1 #set background as whiteset ribbon_sampling, 1Measurement (又一个十分重要的功能，可以真正挖掘结构的意义)dist #测量两个原子之间的距离，ctrl+右键选择第一个原子，ctrl