wwPDB EM Validation Reports Now Publicly Available
The wwPDB archive has now been updated to include validation reports for every released set of EM model coordinates in the PDB and every released EMDB map entry. Validation reports provide quantitative and visual assessments of structure quality and enable archive-wide comparisons (https://www.wwpdb.org/validation/validation-reports).
wwPDB EM validation reports were first made available to OneDep depositors in 2019 (http://www.wwpdb.org/news/news?year=2019#5db841ceea7d0653b99c8839). The current reports are based on recommendations obtained from EM Validation Task Force (VTF) meetings in 2010 (Structure 20: 205-214, wwpdb.org/task/em) and 2020 (white paper in preparation), as well as EM Validation Challenge events (https://www.ncbi.nlm.nih.gov/pubmed/32002441, https://www.biorxiv.org/content/10.1101/2020.06.12.147033v1). Examples of recent improvements include images for deposited masks, improved map-model overlay images, visualization of a (approximate) raw map from two half-maps, and rotationally averaged power spectrum plots. The underlying methodology is continually improved, based on community requirements, requests and feedback.
The PDB Core Archive holds validation reports that assess each PDB model along with its associated experimental map/tomogram from EMDB. EM map+model reports can be downloaded at the following wwPDB mirrors:
- wwPDB: ftp://ftp.wwpdb.org/pub/pdb/validation_reports/
- RCSB PDB: ftp://ftp.rcsb.org/pub/pdb/validation_reports/
- PDBe: ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/
- PDBj: ftp://ftp.pdbj.org/pub/pdb/validation_reports/
The EMDB Core Archive holds validation reports that assess each EMDB map/tomogram entry. EM map-only reports can be downloaded at the following URLs:
- EMDB: ftp://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/
- wwPDB: ftp://ftp.wwpdb.org/pub/emdb/validation_reports/
- RCSB PDB: ftp://ftp.rcsb.org/pub/emdb/validation_reports/
- PDBj: ftp://ftp.pdbj.org/pub/emdb/validation_reports/
If you have any questions or queries about wwPDB validation, please contact us at email@example.com.