Working at home last Thursday, trying to get some quiet time to focus on a review article, I caught the lunchtime news and heard of the untimely death of the actress Wendy Richard. She was best known as Pauline Fowler from long-running BBC soap Eastenders. But those of an—ahem—older generation may remember her more fondly as the ditzy Miss Brahms, one of the bizarre cast of characters from Are you being served?, a 1970s sitcom about the staff of Grace Brothers Department store. Despite the title, service seemed to be the least of the their preoccupations.
Wendy Richards as Miss Brahms
Which is a bit like Open Access sometimes, a topic that crops up frequently, most recently on Caryn Schectman’s blog. It’s supposed to be about serving information more freely to the scientific community (and anyone else who’s interested) but sometimes, although the data are now public (_The truth is out there!_), they’re not always so accessible. I’m not talking about papers—download, print (or perhaps not), read—but all the raw data that are now accumulating at sites around the world. As Heather has mentioned, getting your hands on it is not always that easy.
But returning to my desk last Thursday, I found a very nice example of Open Access working well—for me at least. I wanted to check out a detail in a figure of a protein-RNA complex in one of the papers I was reading. Was that hydroxyl group really in that position I asked myself. I wanted to to have a look at the electron density map that the model had been built into for myself.
And I could, using the Electron Density Server (EDS). Let me explain very briefly: when protein crystallographers publish a new structure these days, they are required to deposit not only the coordinates of the macromolecule with the PDB, the Protein Data Bank, so that anyone can have a look at it on their computer*, but they must also send in the structure factors, colloquially known as F’s. The F’s are basically the raw data and allow you to reconstruct the electron density map that was used to guide construction of the atomic model. But only a seasoned crystallographer would know what to do with them; and even then, there is a bit of an activation barrier between grabbing the F’s and running the programs needed to generate the maps.
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.
Now, it’s still not for everyone. In part that’s because of the nature of the data, since you need to have some understanding of the crystallographic method to be able to interpret the maps. And O does have a bit of a learning curve (though if you can find a friendly local crystallographer, I reckon they could take you through the basics in 10-20 minutes). So, if you’re a neophyte, you would probably want pretty badly to have a look before you had a go. But for the crystallographic community the EDS is a great resource – it serves up the data with a smile.
Now I’m still not ready to run with the radicals of the Open Science movement who want to lay every single pipette action before the public in real time, but—if a result is published—I do want to be able to see the data. The EDS is, I hope, part of a growing movement that is affecting all fields of science. So I look forward to easier access, in all areas.
*Though it’s also an interesting question of how easy it is for non-structural biologists to grapple with pdb files and molecular graphics programs, even when they don’t care about the electron density. Perhaps a topic for another day.
Gerard J. Kleywegt, Mark R. Harris, Jin yu Zou, Thomas C. Taylor, Anders Wählby, T. Alwyn Jones (2004). The Uppsala Electron-Density Server Acta Crystallographica Section D Biological Crystallography, 60 (12), 2240-2249 DOI: 10.1107/S0907444904013253