PyMOL简介及相关操作
To retrieve the color for a residue as identified in an expression, you can either iterate over aselection from the PyMOL command lineiterate all, print colorAlternatively, this can be done from a Python script.import pymolpymol.color_list = []cmd.iterate(‘all’, ‘pymol.color_list....
Command：setattr m residueLabelPos 2 可通过菜单栏Actions>Label对标签的显示样式进行更改，如通过Actions...
PyMOL指导:在PyMOL中查看原始蛋白(5tj3),以cartoon形式查看,将Zn2+原子视为spheres,并将底物模拟残基TPO明显着色(在PyMOL中,尝试select resn TPO)。 创建蛋白质的拉马钱德兰图,比较两种图不同: [Ramachandran plot] [Richardson's Anatomy and Taxonomy of Protein Structure]( import matplotlib # this inline ...
Pymol 使用说明 PyMol Tutorial http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html[2014/6/12 11:19:32][return to KB Wong's home page]Through this tutorial, you will be able to generate the following figures:You can download the files for the tutorials here Files included:1w2...
用pymol来做,pdb没有氢的需要加氢,选肽段,find-polar contacts-to others excluding solvent,all-show lines,手工选取形成氢键的残基,显示为sticks,关闭lines,标记by residue,记录残基号。在pml文件里输入残基号,用命令显示选择内的氢键。 The "polar contacts" mentioned above are probably better at finding hydro...
near_res 选择直接和s1相连的原子 Pymol select vicinos, nbr. resi 10 另外,利用括号可以多重逻辑选择,如选择chain b,但不选择其中的residue 88: Pymol select chain b and (not resi 88) 注:当有多个括号时,Pymol优先处理最里层括号里面的内容。 35 ?关于cartoon ? cartoon的命令格式如下: ? Pymol ...
Chemical-symbol-list 单字母或双字母的化学元素符号 PyMOL>selectpolar,symbolo+n name n. Atom-name-list 蛋白和核酸中至多4字母的原子符号 46、 PyMOL>selectcarbons,nameca+cb+cg resn r. Residue-name-list 3字母的氨基酸符号 PyMOL>selectaas,resnasp+glu+asn+gln 或至多2字母的核甘酸符号 PyMOL>...
def contacts(selection, filename='contacts.png', cutoff=8): # get residue numbers stored.resis = [] cmd.iterate(selection, 'stored.resis.append(int(resi))') # get coordinates stored.positions = [] cmd.iterate_state(1, selection, 'stored.positions.append((x,y,z))') # a little check...
Opensource molecular visualization system. Fork of http://sourceforge.net/projects/pymol/ We provide pymol windows installer for python2.7, for both pymol 1.5 and pymol 1.6 - pymol/pymol/ChangeLog at master · evonove/pymol