Tag Archives: structure

Words fail me

As I’m a biologist, rather than an inorganic chemist or a mineralogist, I don’t have much (well, any) need to look at crystal structures of simple inorganic compounds. Just as well…

…our story begins at Twitter, where David Bradley asks:

Anyone know where to find crystal structures of sodium hypochlorite and sodium bisulfate (cif files or similar) ? #science #crystal

Never thought about it, you say, but surely it can’t be very difficult. So you head to Google and try searches such as “inorganic crystal structure database”. Where you unearth two main players: the Inorganic Crystal Structure Database (ICSD) and the Cambridge Structural Database (CSD). Both are private, requiring registration, login and in one case, installation of an X-client.

Coming from bioinformatics where comparable resources such as the PDB are freely-available via web interfaces, I find this utterly perplexing. Why do these research communities stand for it? Is anyone developing free, open alternatives?

Rapid command-line access to the PDB

This is hardly earth-shattering stuff, but just for reference.

There are multiple ways to grab PDB files from the RCSB PDB servers. If you know the accession code of a structure, the simplest way is wget (or similar) straight off the FTP or HTTP server:

FTP
wget ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdbXXXX.ent.gz

HTTP
wget http://www.rcsb.org/pdb/files/XXXX.pdb.gz

where XXXX is the 4-character PDB accession code.

Note the recent change of URL for the PDB archive: ftp://ftp.wwpdb.org. Note also the confusing 2, not 3 “w” in the URL.

The Protein Structure Initiative: money well spent?

The latest issue of the journal Structure looks at structural genomics.

While the number of structures and impact has been substantive, the cost of the PSI-2 initiative is large. In the US alone, the NIH spends approximately $65 million each year on this effort. As a result, legitimate questions arise as to whether or not the money on PSI is well spent, especially at a time when funding for independent investigator-driven research appears scarce. To facilitate this debate, we will publish commentaries from both supporters and opponents of the structural genomics effort in the next few issues of Structure; we invite any additional comments from readers to be e-mailed to the Editors (structure@cell.com) We believe this debate is especially timely because of the ongoing need to shape PSI-3, which may or may not begin in 2010.

Read the rest…