P212121

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)