Pymol在线高级教程--电子密度图、APBS静电表面制作等
阿里在群里共享了一个Pymol学习的网页，关于A tutorial on using PyMOL to generate publication quality figures.包含：
1. Figure showing Electron Density Map
2. Cartoon representation and surface
3. Using APBS and PyMOL to display the electrostatics surface
4. Create a series of PNG files for animated GIF movie
5. Structural alignment of two homologous proteins
大家可以学习下。
1. Pymol制作电子密度图
1. Loading PDB file
File -> Open -> 1w2i.pdb
2. Load the map file
File -> Open -> 2fofc.map.xplor
It takes a while to load the map file.
3. Zoom in the active site
PyMOL> select active, (resi 14-20,38) and chain A
PyMOL> zoom active
PyMOL> hide all
PyMOL> show stick, active
4. Locate and Display the active site water
We know that the amide group of Asn38 is h-bond to an active water.
PyMOL> select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH)
The above command select any water molecules that is/are around 3.5A of the ND2 atom of resi 38 in chain A
PyMOL> show spheres, active_water
Well the Oxygen atom is now shown in its vdw radius. We can reduce the size of the sphere to 0.5A by:
PyMOL> alter active_water, vdw=0.5
PyMOL> rebuild
5. Display the electron density around the active site atoms at sigma level=1.0
PyMOL> isomesh mesh1, 2fofc.map, 1.0, (resi 14-20,38 and chain A), carve=1.6
Because the residue atoms were previously defined as "active", you can simply type:
PyMOL> isomesh mesh1, 2fofc.map, 1.0, active, carve=1.6
6. You can change the color of the map by:
PyMOL> color grey, mesh1
7. Normally you want to set the background color to white for publication
PyMOL> bg_color white
8. Publication quality figures
To render a figure with the default resolution (640x480)
PyMOL> ray
You will be able to preview the low resolution figures on screen. If you have done everything right, you should be able to see this:
To render a figure with high resolution
PyMOL> ray 2400,2400
Well, it takes a while to produce it. Then you can save the figures in PNG by
File -> Save Image
9. You can save the session by:
File -> Save Session
The saved session will be a .pse extension. You can reload it by double-click the .pse file in Windows.
网页地址：http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html 那个网址看不了，楼主有没有保存，求发3. Using APBS and PyMOL to display the electrostatics surface 川大-灰太狼 发表于 2019-2-26 10:17
没有明白你的“基因组”的基因 是什么意思，是 碱基吗？一般标记可以用Label 命令。 ...
是这么回事~我从GEO数据库中获取了一个基因组的3D结构，该结构包含5条染色体，为PDB格式，Pymol可以打开。同时，数据库中还提供了各个染色体上接近100多个基因的XYZ轴坐标，这一坐标文件是TXT格式。我现在就是想利用Pymol把这100多个基因显示在染色体的3D结构上，显示的基因标注成其他颜色。然后我用label命令试过，发现标注的文字及位置根本不在染色体上，不管我怎么输入坐标，最后标定的点都在基因组3D结构的几何中心，应该还是我哪里命令错了吧 囧rz 还请指点一二！先谢谢啦！ 风姿花传 发表于 2018-10-30 16:55
谢谢分享
大神说的是哪个群啊 想加群
BioMS的官方群，现在群人数接近2000，本论坛服务于生物分子模拟群，仅对群会员开放，如需注册请先加入群，待认证后批准加入论坛会员！生物分子模拟QQ群：68093966
支持:):):):):):):):):):):):) 本来想评个分的，但提示说这不属于我管辖的范围！ 好好的福利贴~~~:D qian430 发表于 2013-12-21 16:58 static/image/common/back.gif
请问，蛋白active site和ligand的电子密度图在我们计算领域能分别说明那些问题，或解释那些现象？ ...
其实电子密度图才是近似真实的分子形状。所以他们有对电子密度进行RMSD计算的，从而来与实验得到的电子密度形状比较。电子密度图相似的，则更可能是有效的抑制剂。 qian430 发表于 2013-12-24 20:51 static/image/common/back.gif
对电子密度进行rmsd？这个好神奇呀，哈哈，你是不是想说比较电子密度比计算rmsd更精确 ...
就是比较电子密度图的叠合情况：） 请问MAP文件在哪里可以下载哇 这个文件是哪里来的啊.map.xplor “2fofc.map.xplor” 这个文件哪里下载呀，谢谢！ 漂亮 :loveliness:
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