Display Electron Density Map from the EDS in Pymol
1) Go to the electron density server
2) Save the map in CCP4 format.
Note: if you save the map as an ‘XPLOR’ or ‘CNS’ file, you will need to rename the extension ‘.xplor’. This will enable you to extract the files you have just downloaded.
Example: 1w5x.cns -> 1w5x_2fo-fc.xplor
(I like to enter in the type of map (2fo-fc) as soon as I download it)
-If you do not change the extension, pymol will not recognize/see the file when you are searching/browsing.
3) Load pdb that corresponds to the map you downloaded into pymol
Example: 1w5x.pdb
4) Diplay -> Background -> white
5) H-> everything S-> sticks
6) Load the map that was downloaded from the electron density server into pymol.
Example: File -> Open -> 1w5x.ccp4
You will still NOT see electron density, you need to use the mesh command next (see image below).
7) Mesh Displayed:
If you don’t want your structure looking like clown vomit, enter the following into the command line:
isomesh mesh1, 1w5x_2fofc
9) mesh1 -> C -> grays -> gray70
(see how to use the electron density server post for a publication)
Matt k
June 30th, 2009 at 9:53 PM #
I believe mesh as portrayed is showing a wireframe surface of the pdb file, not contouring the electron density map. The fact that sticks, lines spheres etc are options in the drop down menu is indicative of the pdb file (with a map the options should be mesh/surface/slice). The mesh inherits atom colours from the atoms, hence its rather colourful appearance. To make a density map using the drop down menu you can use the mesh option associated with the map, but using the density wizard is much more practical as it allows you to control the map size so you can ray trace without crashing.
Nice to have someone blogging about crystallography, btw. I’m amazed that you find the time.