2024-07-17 : 37051 EMDB map entries, 21507 PDB coordinate entries RCSB PDB | PDBe

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 (link).

wwPDB EM validation reports were first made available to OneDep depositors in 2019 (link). The current reports are based on recommendations obtained from EM Validation Task Force (VTF) meetings in 2010 and 2020 (white paper in preparation), as well as EM Validation Challenge events sponsored over the past decade by EMDR (see also our preprint describing the 2019 EMDR Model Challenge outcomes and recommendations*). 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.

Read the full January 12, 2021 wwPDB news item with links to worldwide EM validation report mirror sites here.

*A revised version was accepted for publication in Nature Methods in late December and is now in press.

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