Electron Density Server
***see comments for now even a faster way***
Electron Density Server (EDS) provides the scientific community with a service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. The reference for using the server can be found here.
Why would being able to quickly view electron density maps be helpful?
Allows others to gain a deeper understanding/appreciation of your interpretation of how the structure should be built. I have read papers which state something along the lines of “density was missing so I can’t build a given loop.”
Well, how much density was missing? Do you know the carbon alpha locations, but not the slide chains? etc…
Overall, this tool allows for a method to validate a give crystallographic structure. A more complete discussion of the need for the deposition of structure factors can be read in the above reference.
Here are the steps to use the server (it is not hard):
1) submit desired PDB ID into server
2) Left hand side is a ‘Downloads’ section
3) Click on ‘Download maps’
4) Select map format
-if you are using Coot then download either the ccp4 or cns format
5) Select type and download
6) Double click on .gz file, which will cause the files to open in a folder
7) Highlight desired file then click ‘extract’ usually in the upper part of the window
Finally, Open Coot -> File -> Open Map…
If you need the coordinates (where the atoms are located, sometimes called a pdb file since that is its extension) you can download it at the EDS.
There a number of neat options in the EDS, but they will have to wait for another post.
Stephen Curry summed up the real life application of the EDS quite well:
Thanks to the Electron Density Server, it took me all of 30 seconds to go from “Hmm, I’d like to check that out” to “Oh, I see what they mean.” On the EDS web-page you simply enter the PDB identifier for the structure (taken from the paper) and it immediately serves up a package of files that, once unzipped, lets you fire up the molecular graphics program O. You can then get straight to work: in the O session the structure coordinates and maps are already loaded. The EDS is a fantastic piece of work.
Kind of sounds like a clip from an infomercial.
As a side note you can check out Stephen’s blog here, which is an interesting blend of real and reciprocal space.
Stephen Curry
March 10th, 2009 at 4:02 PM #
Great post (and thanks for the plug). Just to let you know that there is no need to divert to the pdb to get the coordinates since the EDS serves these up along with the maps (see the download menu).
admin
March 10th, 2009 at 4:26 PM #
Thanks, I will update the post to keep it as stream lined as possible.
Paul Emsley
April 28th, 2009 at 12:50 PM #
Oh, I’m a bit late to this one… but for the record, it’s easier to use EDS and Coot than you suggest. Simply:
File -> Get PDB and Map using EDS…
(no need to use the web browser if you know the accession code).
(Coot actually downloads the MTZ file and does the FFT internally – which is faster than getting the map. Gerard Kleywegt helped me get this working).
admin
April 29th, 2009 at 10:28 PM #
Awesome.
You should have a slogan with your name:
Paul Emsley – Try to Keep up