浏览完整代码 来源:findSurfaceResidues.py 项目:BioinformaticsArchive/mqap 示例18 def _testSpectrum_setup(self): cmd.pseudoatom('m1', pos=(-2,0,0)) cmd.pseudoatom('m2', pos=(0,0,0)) cmd.pseudoatom('m3', pos=(2,0,0)) cmd.show_as('spheres') self.ambientOnly() cmd.viewport(40,...
Pre-selection of surface-exposed atoms is managed by a cutoff using the calculated solvent-accessible surface area for each atom. This pre-selection is set by a user-provided cutoff and is integrated in PyTMs. The original procedure is described on the PyMOL wiki (`findSurfaceResidues’). ...
是的,这东西叫属性选择符,列表如下属性选择符缩略形式标识符和举例symbole.Chemical-symbol-list单字母或双字母的化学元素符号PyMOL>select polar,symbol o+nn amen.Atom-name-list蛋白和核酸中至多4字母的原子符号PyMOL>select carb ons,n ame ca+cb+cgresnr.Residue-name-list3字母的氨基酸符号PyMOL> 20、...
1. L->residue 在α碳原子上标记其残基名字和编号 (常用) 2. L->residue name 在所有原子上标记残基名字 (不常用) 3. L->clear 删除该对象上所有的Label 4. L->element symbol 显示对象上所有原子的元素名字 5. L->vdw radius 产看原子的范德华半径 ...
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...
protein atoms # `create`: creates a new molecule object from a selection. It can also be used to create states in an existing object.# `create name, (selection)`# 3. Display created surface # 4. Set color for surrounding_res # 5. Set transparency for surrounding_res ...
The best combination I can find is:set ambient=0set direct=0.7set reflect=0.0set backface_cull=0Which gives no shadows and only a few artifacts.As an alternative, you might just consider showing the inside of the surface directly…that willcreate less visual artifacts, and so long as ...
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...
ss 4. Color chain A and B •color blue, chain A color red, chain B 5. Create a surface display for chain A and chain B •create obj_ab, chain A or chain B •show surface, obj_ab 6. Find and Color the active site residue select zn, resn ZN and obj_ab show...
Pre-selection of surface-exposed atoms is managed by a cutoff using the calculated solvent-accessible surface area for each atom. This pre-selection is set by a user-provided cutoff and is integrated in PyTMs. The original procedure is described on the PyMOL wiki (`findSurfaceResidues’). ...