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582 bytes added ,  12:37, 21 October 2009
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==== Relation between R and R<sub>free</sub> as a function of resolution ====
 
==== Relation between R and R<sub>free</sub> as a function of resolution ====
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* The PDBe provide a service to plot many different statistical properties in the PDB against other properties. The link is http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp . You can see that there is an option of RDiff which is the difference between R and R-Free for all structures that contain both data.  Take a look at this first. There is a second parameter which you can set to resolution and this will allow you to draw a plot that you want. This will draw a 3D isometric plot which you can scale, and pick data points to view particular entries.
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* formula from Kleywegt and Jones (2002): R<sub>free</sub> = 1.065*R + 0.036
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* plot with empirical data: http://xray.bmc.uu.se/gerard/supmat/rfree2000/rfminusr_vs_resolution.gif
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* many more plots: http://xray.bmc.uu.se/gerard/supmat/rfree2000
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* harry plotter (java): http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
    
References:
 
References:
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* GJ Kleywegt and TA Jones (2002). Homo Crystallographicus - Quo vadis? Structure 10, 465-472. (reprint from http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=65)
 
* GJ Kleywegt and TA Jones (2002). Homo Crystallographicus - Quo vadis? Structure 10, 465-472. (reprint from http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=65)
- formula from that paper: R<sub>free</sub> = 1.065*R + 0.036
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- plot with empirical data: http://xray.bmc.uu.se/gerard/supmat/rfree2000/rfminusr_vs_resolution.gif
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- many more plots: http://xray.bmc.uu.se/gerard/supmat/rfree2000
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- harry plotter (java): http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
      
== what kinds of problems exist with these indicators? ==
 
== what kinds of problems exist with these indicators? ==
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