• PyMOL> color blue, chain B Create a surface display for chain A PyMOL> create obj_a, chain A PyMOL> show surface, obj_a Color the active site residue PyMOL> select active, (resi 14-20,38 and chain A) PyMOL> color yellow, active PyMOL> turn y, -60; turn x, -20 PyMOL...
1）set transparency, F, selection （F：0.0-1.0的浮点数）
set surface_carve_selection, ligand step3 设置口袋的大小 set surface_carve_cutoff, 5 step4 设置口袋的表面的透明度 set transparency,0.3, 1azm_e_chg step5 切换为溶剂可接触表面 set surface_solvent, 1 删除配体分子5A以外的水分子 remove resn hoh and (resi 307 gap 5) 删除极性氢原子 remove ...
调整Transparency-cartoon为80%突出活性位点,对活性位点添加标签,结果如下图。 Thr Cys Arg Electrostatic surface representations 1.溶剂可及表面图:利用Pymol软件打开目的序列的pdb文件,选择APBS Electrostatics,选择范围为±3.5,得到溶剂可及表面图。利用相同方法,对同源序列的可及表面图进行绘制。 2.目的溶剂排除表面...
object.# `create name, (selection)`# 3. Display created surface# 4. Set color for surrounding_res# 5. Set transparency for surrounding_res# Transparency is used to adjust the transparency of Surfaces and Slices.# `set transparency, F, selection`#show surface, 1hsgcreate surrounding_res, ...
首先:Pymol> show representationPymol> hide representation其中 representation 可以为: cartoon, ribbon, dots, spheres, surface mesh。使用这2个命令可以让Pymol以不同得方式显示蛋白质结构。例如当我们键入:Pymol> hi 14、de linesPymol> show ribbon我们将得到如下结果:也许您已经注意到结构中有2个一模一样...
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2002/07/25 [PyMOL] Object-specific transparency Gareth Stockwell 2002/07/24 [PyMOL] Suppress some output kkliang 2002/07/24 [PyMOL] Réf.: [PyMOL] Up & down arrow problem under OSX joergli 2002/07/23 [PyMOL] Re: PyMOL-users digest, Vol 1 #124 - 1 msg Brian Swalla 2002...
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bg white//背景改为白色assurface,3oc0//显示大分子表面color white,3oc0//将颜色改为白色settransparency,0.5//设置透明度为50% 点击右侧控制台的lig对象的C项,选择by element,碳原子为cyan。 image 将我们需要的氨基酸残基复制到新对象中 create residues, (3oc0 in resi 205+206+631+656+659+662+666) ...