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
validat...@mail.wwpdb.org
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: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
________________________________
________________________________
De : Gerard DVD Kleywegt <ger...@xray.bmc.uu.se>
? : CCP4BB@JISCMAIL.AC.UK
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 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
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************
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 !
******************************************************************
