Electron Density Map Help

To obtain electron density maps you must enter a PDB code into the entry field and press

the "Get Map" button.

Not all PDBs are supported, but many are. Once the page has loaded you must change the

"Map Format" to CCP4 or O but don't change "Type", click "Generate map".

Once it has created your file right click the file link that is generated and select

"Save link as" and save the gunzip file to a location you remember.

Unzip it with WinRAR or WinZip and rename it or else it will replace the PDB file in

the viewer when you try to open both. The addition of "map" is suggested (ie. 1taumap.ccp4).

Now load the electron density map using the "Load Map" option under the “Electron Density Mapping”.

In EZViz, insert your own name for the object in "Name Object" for easier manipulation of single and

multiple maps, and enter the filename of the map underneath it for Pymol to recognize it.

Then select a viewing method and click on it. If you wish to superimpose the map over a regular

PDB structure you must also load the regular PDB as well.

Mesh, Dot, Surface, and Roving Mesh can be used with or without a PDB file present in the viewer,

while Mesh Selection, Dot Selection, and Surface Selection all require a PDB to be present, as well

as the user to have made an atom selection on the protein. The selection cannot be renamed and must remain ‘sele’.

This will superimpose the map over only selected areas of the PDB protein.