<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Updated validation reports for all X-ray, NMR, and 3DEM structures released in the PDB archive are now available.<br class=""><div class=""><p class="">The
updates include new percentile statistics reflecting the state of the
PDB archive on December 31, 2019 and calculated map coefficients used
for validation report generation.</p><p class="">The updated reports are accessible from the following FTP sites:</p><ul class=""><li class=""><a href="ftp://ftp.wwpdb.org/pub/pdb/validation_reports/" class="">ftp://ftp.wwpdb.org/pub/pdb/validation_reports/</a> (wwPDB)</li><li class=""><a href="https://urldefense.com/v3/__ftp://ftp.rcsb.org/pub/pdb/validation_reports/__;!!Mih3wA!WsKGiqy6Bg-WQ9I05uACc09P-IMv5hZ3-ep8QBoxd4AiiM59LFhYhqQYPBuxuBd1lA$" class="">ftp://ftp.rcsb.org/pub/pdb/validation_reports/</a> (RCSB PDB)</li><li class=""><a href="https://urldefense.com/v3/__ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/__;!!Mih3wA!WsKGiqy6Bg-WQ9I05uACc09P-IMv5hZ3-ep8QBoxd4AiiM59LFhYhqQYPBs4s9R0TQ$" class="">ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/</a> (PDBe)</li><li class=""><a href="https://urldefense.com/v3/__ftp://ftp.pdbj.org/pub/pdb/validation_reports/__;!!Mih3wA!WsKGiqy6Bg-WQ9I05uACc09P-IMv5hZ3-ep8QBoxd4AiiM59LFhYhqQYPBsRkNnvQQ$" class="">ftp://ftp.pdbj.org/pub/pdb/validation_reports/</a> (PDBj)</li></ul><p class="">A snapshot of the previous version on June 10th is archived at <a href="ftp://snapshots.wwpdb.org/20200610/pub/pdb/" class="">RCSB PDB</a> and <a href="https://urldefense.com/v3/__ftp://snapshots.pdbj.org/20200610/pub/pdb/__;!!Mih3wA!WsKGiqy6Bg-WQ9I05uACc09P-IMv5hZ3-ep8QBoxd4AiiM59LFhYhqQYPBtjcPH1Tw$" class="">PDBj</a>.</p><p class="">These
updated wwPDB validation reports provide an assessment of structure
quality using widely accepted standards and criteria, recommended by
community experts serving in <a href="https://www.wwpdb.org/task/validation-task-forces" class="">Validation Task Forces</a>.</p><p class="">In
addition to recently introduced carbohydrate section and 2D Symbol
Nomenclature For Glycan (SNFG) images for oligosaccharides from the <a href="https://www.wwpdb.org/documentation/carbohydrate-remediation" class="">carbohydrate remediation project</a>, these reports now incorporate <a href="https://www.wwpdb.org/news/news?year=2019#5cfa7992ea7d0653b99c87d0" class="">visualization</a>
of ligand validation and model fit to electron density maps for X-ray
ligands. These include 2-dimensional diagrams of ligands, highlighting
geometric validation criteria and, for structures determined by
crystallography, 3-dimensional views of electron density.</p><p class="">In addition, <a href="https://www.wwpdb.org/news/news?year=2019#5db841ceea7d0653b99c8839" class="">EM map analysis</a>,
and the fit of EM model to its map volume. FSC curves are also included
to compare reported and estimated resolution, where either half maps or
FSC data was uploaded.</p><p class="">Validation reports are provided to
depositors through OneDep - the wwPDB portal for validation, deposition
and biocuration of structure data. The wwPDB partners encourage the use
of the <a href="http://validate.wwpdb.org/" class="">stand-alone validation server</a> and the <a href="https://www.wwpdb.org/validation/onedep-validation-web-service-interface" class="">web service API</a>
at any time prior to data deposition. Depositors are required to review
and accept the reports as part of the data submission process.
Validation reports will continue to be developed and improved as we
receive recommendations from the expert <a href="https://www.wwpdb.org/task/validation-task-forces" class="">Validation Task Forces (VTF) for X-ray, NMR, EM</a>, and as we collect feedback from depositors and users.</p><p class="">The
wwPDB partners strongly encourage journal editors and referees to
request reports from authors as part of the manuscript submission and
review process, as already required by <i class="">Nature, eLife, The Journal of
Biological Chemistry, the International Union of Crystallography (IUCr)
journals, FEBS journals, Journal of Immunology</i> and <i class="">Angew Chem Int Ed Engl</i>. Reports are date-stamped, display the wwPDB logo, and represent standardized wwPDB validation.</p><p class=""><a href="https://www.wwpdb.org/validation/validation-reports" class="">Further information and sample validation reports are available at wwpdb.org</a>.</p><p class="">Your feedback, comments, and questions are welcome at <a href="mailto:validation@mail.wwpdb.org" class="">validation@mail.wwpdb.org</a>.</p><div class=""><br class=""></div></div><div class="">Source: <a href="https://www.wwpdb.org/news/news?year=2020#5f6377df07302466657ec0df" class="">https://www.wwpdb.org/news/news?year=2020#5f6377df07302466657ec0df</a></div><div class=""><br class=""></div></body></html>