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CCP4BB  April 2013

CCP4BB April 2013

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Subject:

Re: Off-topic: PDB statistics

From:

Tim Gruene <[log in to unmask]>

Reply-To:

Tim Gruene <[log in to unmask]>

Date:

Mon, 15 Apr 2013 16:04:48 +0200

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Dear Raji,

the numbers you have accumulated might already be accurate, it is more
a question of how precise your numbers should be - and this might
become a long discussion without resulting in a single answer:

Take into account that the PDB query relies on the entries in the PDB
headers. And take into account that it might not be clear e.g. what is
a MR solution: If I solved a structure with a new ligand and get the
phases from refining the new data against the protein without ligand,
you might call this MR, although personally I think of the search for
the correct placement in the unit cell when I speak of MR, so in this
case it is not really MR. Other people will have different opinion
about this and so forth.

Best,
Tim

On 04/15/2013 03:48 PM, 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?
> 
> Thanks much. Raji
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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