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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
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 |
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发表于 2013-9-27 08:53:13
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发表于 2016-3-26 16:15:05
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