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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=ae7f982d2df966a2f95f73a794d46efffb16c227a75389fdd058f5cc62d1654d
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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=eaa2ef06948e08de06b7fbd47cbfe0ec2c5dac82a4c70b2ffd055bbdf10311ec
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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=106d86fcfd3fb5e631ca04b4d6f0be2adb8a60edf33ca698248517e47de9e5c7) 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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=455ace0917c519ea7f631e3906413c60cf63deb9c4512491003cebf397e148d0).
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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=88f1dd8be8660e1657bae27e311478f5ed3dfbd2922c198277688efbe98e7ba1 - 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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=26d1c36fa29104dc85265fe4997ceaafec2e797dded7fb1ea2e39ae02988262a
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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=3f324c797061411513168635757d7fc61545406ac5203d849b72a712bbe5e644
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=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=3f50278f4e3251a6c6efc1d0f293bed530f5fb4bcd94ef2a6426d1fbcffdfc7c
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
