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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=494f114fbff8c5913722a563f0fac87daa91b4a0943e65f0c0d0258697324e71
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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=ceb8a826f9fd1bcb945c2d5d2108bfcd5af42fb57dd42c876d8e434f7e44302f
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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=c36bb823c5eab11a764ba159a174b979be73b6a5afb1bdcd821b991dd813850d) 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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=09ba089e02bd4ac32ff47acb46f1659bfc50fd8dbf4b0064917cc1622f5bc36f).
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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=30a7f6e1086c7cf681d793b223a5f56a794439dc12a51b952b7ee69db0dfd24f - 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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=8384ec2d0000e5f88f578d48e541831c47161606776d3787393f20fc9c6a59d4
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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=0af71922028784db5dee672128cc8d1a9131aba3b56f4777dc2bcbaa15c96a2c
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=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=4fe494878b502d19dedc40a0cfdeded207b166ca483a0d06643466303b4146b5
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
---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
[log in to unmask] ..................... pdbe.org
Secretary: Pauline Haslam [log in to unmask]
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