How to display Electron Density Server results in PyMol

Apr 16, 2009

1) Go to the Electron Density server and enter you desired PDB code (1c8u in this example)
electron density server How to display Electron Density Server results in PyMol

2) Download the coordinates, followed by the map in CCP4 format
electron density server map How to display Electron Density Server results in PyMol

3) Extract the files that you downloaded
(7-zip will work for windows if you do not already have it installed)
**Rename using the term map: example) 1c8u.ccp4 renamed to 1c8u.map.ccp4

4) Start PyMol and open the pdb and map files (File -> Open)
pymol How to display Electron Density Server results in PyMol

5) Display the map by clicking on the ‘A’ for actions then mesh followed by selecting your desired mesh level – as shown above (I did 2.0 in this example)

-Below: if you look at the upper right corner you can see what is displayed by if it is highlighted (light gray) in the PyMol window (in this case 1c8u.map is off)
pymol mesh How to display Electron Density Server results in PyMol

6) Enter the information available on the PyMol Wiki into the command line (enter everything left of the # symbol)

select site, resi 39-50 # residues that are displayed for viewing
isomesh map, 1c8u.map, 2.0, site, carve=1.6 #display the map around the selected residues (change 1c8u.map to correspond to how you named your .map file)
pymol selection How to display Electron Density Server results in PyMol

color grey30, map # sets map to 30% gray
bg_color white #sets background to white
set ray_trace_fog, 0 #turns off raytrace fog–optional
set depth_cue, 0 # turns off depth cueing–optional
set ray_shadows, off #turns off ray-tracing shadows

I then zoomed in on one of the selections then showed ‘S’ ’sticks’ in the PyMol window.

7) Click on ‘ray’ for ray tracing then followed with ‘color grey30, map’ since the mesh looked black (note again what is toggle on and off in the upper right)
pymol presentation How to display Electron Density Server results in PyMol

8) Finally, you can add labels using GIMP or Photoshop

Don’t forget to cite PyMol

If you would like to learn how to easily make a movie using PyMol check this post out.

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3 Awesome Insights so far | Have Your Say!

  1. Kenric
    September 14th, 2009 at 8:45 PM #

    I have no idea what this is, but it looks really cool.

  2. Sean
    September 14th, 2009 at 8:51 PM #

    It is. :)

    If you are the Kenric that I am thinking of – go update your blog it has been almost a week.

  3. JVertrees
    April 5th, 2010 at 2:03 AM #

    Great tips. A couple other useful commands/settings for this:

    # make thinner mesh
    set mesh_width, 0.65
    # more vertices
    map_double mapName, *

    Lastly you can fetch maps directly from the EDS server with:

    fetch pdbID, type=fofc

    or

    fetch pdbID, type=2fofc

    – Jason

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