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:

          http://pdbe.org/1cbs

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 http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf).

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:

          http://pdbe.org/1cbs/downloads

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.:

          http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs

Please send any comments, questions or suggestions on the new style validation reports to [log in to unmask]

Questions about PDBe-specific pages and services can be sent to [log in to unmask]

--Gerard

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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
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Secretary: Pauline Haslam  [log in to unmask]