Bonjour Philippe,
The reports are based on the recommendations of the wwPDB X-ray validation
task force - see http://www.wwpdb.org/workshop/2011/index.html and the report
published by this task force at
http://www.cell.com/structure/abstract/S0969-2126%2811%2900285-1
Of course, if you have specific suggestions for improvements, we'd be
interested to hear from you - feel free to mail them to
[log in to unmask]
A stand-alone server already exists - see
http://www.wwpdb.org/validation-servers.html - hope this turns your Good
Friday into a Great Friday :-)
Best wishes,
--Gerard
On Wed, 16 Apr 2014, Philippe BENAS wrote:
> Dear Gerard CD/DVD/Blue Ray (;-) ),
>
> Yes, these new reports are great although they should/will improve over time.
>
> Another point that would be also really helpful would be to have the opportunity to run the associated scripts either locally or on a remote server from the PDB, prior to the submission itself. Hence they should provide strong guidelines the crystallographers during their rebuilding/refinement stages. I know Phenix for instance has already some of these tools, but not all.
>
> Could the PDB provide something in that way for the everyday use of a poor X-ray crystallographer ?
>
> Best regards,
> Philippe
>
>
>
> ________________________________
> Philippe BENAS, Ph.D.
> X-ray diffraction and computing facilities manager
>
> Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
>
> E-mails: [log in to unmask], [log in to unmask]
> URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
>
>
> ________________________________
>
>
>
>
> ________________________________
> De : Gerard DVD Kleywegt <[log in to unmask]>
> ? : [log in to unmask]
> Envoy? le : Mercredi 16 avril 2014 19h01
> Objet : [ccp4bb] Validation reports for all X-ray structures in the PDB
>
>
> 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 [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]
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:[log in to unmask]
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to actual opinions, living or dead, is purely coincidental.
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Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
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