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
>
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