On Mon, 15 Apr 2013, Raji Edayathumangalam wrote:
Hi Folks,
Does anyone know of an accurate way to mine the PDB for what percent of total
X-ray structures deposited as on date were done using molecular replacement? I
got hold of a pie chart for the same from my Google search for 2006 but I'd
like to get hold of the most current statistics, if possible. The PDB has all
kinds
of statistics but not one with numbers or precent of X-ray structures deposited
sorted by various phasing types or X-ray structure determination methods.
For example, an "Advanced Search" on the PDB site pulls up the following:
Total current structures by X-ray: 78960
48666 by MR
5139 by MAD
5672 by SAD
1172 by MIR
94 by MIR (when the word is completely spelled out)
75 by SIR
5 by SIR (when the word is completely spelled out)
That leaves about 19,000 X-ray structures either solved by other phasing
methods (seems unlikely) or somehow unaccounted for in the way I am searching.
Maybe
the way I am doing the searches is no good. Does someone have a better way to
do this?
There is no way to tell the PDB "I already had phases for this structure
because
it's just a soak or co-crystallization of a new ligand in a well-studied crystal
form." Sometimes those are labeled as "MR" sometimes "isomorphous" sometimes
some other string no label at all. I have tried annotating such depositions as
"known structure" but it gets changed to something else. Anyhow I could easily
believe there are 19000 of these.
Ethan
Thanks much.
Raji
--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University
