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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=a4ec416976c036dba11dd2eba52f58ea7623cf9c77878158a2d68f57c854ea56
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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=e31ebbe11650822dcddc95c8d732073824315aaa1ef0a85f6947ca3e78d08cfe
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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=bb14504b68d5ac31e4d37c4a21b543c89a6fe18fac33b6c8b54db86869a541dd) 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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=9cfce1c69787f7b3b8c7aed8266cbc1a2f80474cd3a0e092aa23b32b22482dcf).
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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=899dc883a72c9aefd1cfa143a8a33e2ecc7bc1a7b0e3b42563c71730ddb8d141 - 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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=696eccc3065b76804f94f1b2ec49a7deede7cfe02e2251290f6a6d246cbaedff
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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=3777dd064f5a5c7afd82c5e78bf77dc52fd85428c524d2083cd96316c6ff3527
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=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=f8067c0121d03f420ec913cd927ad5a65c0bc1831b03ed4e43197317a3228336
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
