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 validation from mail.wwpdb.org
Questions about PDBe-specific pages and services can be sent to
pdbehelp from ebi.ac.uk
--Gerard
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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_admin from ebi.ac.uk
