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 https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=4105ff6448d5bdbd51e474e89f5a06ee532f480bdcd7c0205ce5c6d91b48300e
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:
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=032b800b3e9b3f00999a10131c588183b134c5a44c0c6d5dafd999b619326c1e
you will see the "percentile sliders" displayed in the PDBportfolio widget
(https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfolio&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=66fbe101d6708d887924bdc5bf25021570f9885c97daf3d064f9f7258c3303ad) 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
https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=1e6916c73273cdcf0e20a5b7d4ff23d7961c1d97a12988b072d32fcec45e7570).
If you are not yet familiar with these new style validation reports, have a
look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=fd35f5139833bb5700372d7bf5f2398f28706b2154d8bc1d907eef9e82ac517f - in particular the
user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=11887d82818aef793f525049cf3b75a603cecba6cb0d7351fb3122b50d963f5a
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:
https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloads&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=83fb53eb3391a94d7ad7de7d2fcd02804657e56c7c0b5fb8aa3d655715d9a966
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.:
https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=57e3ff9f13e2ce786081e6f02d66213a2911f3d14ba6003a495ea2d5dd9c1650
Please send any comments, questions or suggestions on the new style validation
reports to validat...@mail.wwpdb.org
Questions about PDBe-specific pages and services can be sent to
pdbeh...@ebi.ac.uk
--Gerard
---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
