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[Pymol] Pymol在线高级教程--电子密度图、APBS静电表面制作等

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发表于 2013-9-27 08:53:13 | 显示全部楼层 |阅读模式

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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
tutorial_1.png
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:
screen1.gif
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

评分

参与人数 1金币 +10 贡献 +1 收起 理由
hinry_jay + 10 + 1 赞一个!很实用!

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发表于 2016-3-26 16:15:05 | 显示全部楼层
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
 楼主| 发表于 2018-11-1 22:04:31 | 显示全部楼层
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

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发表于 2013-9-27 09:17:06 | 显示全部楼层
支持:):)
发表于 2013-9-27 10:32:31 | 显示全部楼层
本来想评个分的,但提示说这不属于我管辖的范围!
发表于 2013-12-15 00:55:31 | 显示全部楼层
好好的福利贴~~~
发表于 2013-12-21 16:58:49 | 显示全部楼层
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?
 楼主| 发表于 2013-12-23 08:49:47 | 显示全部楼层

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。
发表于 2013-12-24 20:51:36 | 显示全部楼层
川大-灰太狼 发表于 2013-12-23 08:49
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 ...

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
 楼主| 发表于 2013-12-24 21:17:57 | 显示全部楼层
qian430 发表于 2013-12-24 20:51
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:)
发表于 2013-12-25 10:33:20 | 显示全部楼层
川大-灰太狼 发表于 2013-12-24 21:17
就是比较电子密度图的叠合情况:)

恩恩,谢谢太狼的回复。嘿嘿
发表于 2015-2-27 11:35:43 | 显示全部楼层
请问MAP文件在哪里可以下载哇
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