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[X-plor] Validation reports for all X-ray structures in the PDB

Gerard DVD Kleywegt via x-plor%40net.bio.net (by gerard from xray.bmc.uu.se)
Wed Apr 16 12:02:28 EST 2014

Hi all,

You may not have noticed, but 19 March 2014 was VR Day - the day that new style 
wwPDB validation reports for all X-ray structures were made publicly available 
- see http://www.wwpdb.org/news/news_2014.html#18-March-2014

The validation-related files for individual X-ray PDB entries can be accessed 
through the web sites and ftp sites of the various wwPDB partners. Speaking for 
PDBe, if you go to the summary page of an X-ray PDB entry, for instance:


you will see the "percentile sliders" displayed in the PDBportfolio widget 
(http://pdbe.org/portfolio) on the right of the page. (Clicking the big white 
arrow will start a slideshow of images related to this entry.) The legend of 
the percentile-slider plot contains a direct link to the validation report (as 
a PDF file; in this case 

If you are not yet familiar with these new style validation reports, have a 
look here: http://www.wwpdb.org/validation-reports.html - in particular the 
user guide may be of interest: http://www.wwpdb.org/ValidationPDFNotes.html

If you want to download the full report (which lists all outliers for many of 
the validation criteria, instead of just the worst 5 or the first 5), or a 
graphic image of the percentile-slider plot, or an XML file with all validation 
data in machine-readable form, go to the downloads page of any X-ray PDB entry, 
either through clicking the "Downloads" link in the menu on the left, or 
directly by going to a URL of the form:


The section labelled "Validation" of the table provides the relevant links.

Note that sites that include PDBportfolio in their pages now automatically 
display the percentile-slider plot and download link as well! To see this in 
action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.:


Please send any comments, questions or suggestions on the new style validation 
reports to validation from mail.wwpdb.org

Questions about PDBe-specific pages and services can be sent to 
pdbehelp from ebi.ac.uk


Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin from ebi.ac.uk

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