[phenixbb] wwPDB X-ray validation task force update

[Randy Read]

Dear CCP4 and Phenix BB subscribers,

The worldwide PDB X-ray validation task force is being reactivated to consider what updates need to be made to the validation criteria that are reported and the validation reports that are produced when you either deposit a new structure or use the standalone wwPDB validation server.  

We're already aware of a number of issues.  Probably the biggest single issue is improving the validation of ligands, including numerical and visual analysis of fit to density.  There's a lot of room for improvement of the validation of carbohydrates.  Our agenda also includes discussions on metals, radiation damage and cis-peptides, among other topics.

The task force will be meeting this coming Monday and Tuesday, so now would be a good time to provide feedback on the current state of the art and in particular on any aspects that I've left out of that list of the topics we'll be discussing.

If you have constructive suggestions on any aspect of X-ray structure validation at the wwPDB, I would be happy to collect any emails I receive and convey them to the rest of the task force.  It's also possible to send feedback at any time through the official channel by an email to validation at mail.wwpdb.org.

* Are there current validation criteria that should be retired in favour of other criteria?

* Are there missing criteria that should be added?

* Are there ways in which the presentation of the validation results in the report could be clarified?

Best wishes,

Randy Read
 
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk