Validation Analysis
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Validation Analysis (VA; Wang et al., 2022) is a collection of EMDB resources for validation of cryo-EM structures, focussing on the quality of the volume data alone and that of the fit of any atomic models (themselves archived in the PDB) to the volume data. VA information for all EMDB entries is available here on the EMDB website. The software can also be run locally, either as part of CCP-EM or by installing the software yourself. For a detailed description of the VA resource, please see the publication. For more information on individual validation components, see the documentation.
If you use the VA resource, please cite: Wang, Z, Patwardhan, A, Kleywegt, GJ (2022). “Validation analysis of EMDB entries”, Acta Cryst. D78, 542-552 (DOI: 10.1107/S205979832200328X)
Three levels of validation information
Based on recommendations from community experts (Kleywegt et al, to be published), the EMDB validation resources are organised in three tiers:
- Tier 1: extensive and evolving set of validation metrics, including tried and tested as well as more experimental ones. This is mainly aimed at specialists in cryo-EM and validation. To access the Tier 1 information for a certain entry, you can use the redirection box on the top of this page and enter the EMDB accession code or type the url into your browser like the following example. The results are presented, separately for each EMDB entry, in the VA web resource, for example: https://www.ebi.ac.uk/emdb/va/EMD-11145/
- Tier 2: a subset of Tier 1 containing metrics that have been tested and are considered to be useful. This is mainly aimed at users of EMDB data. Tier 2 information of each EMDB entry can be accessed from its own entry page. The "Validation" tab will give corresponding validation on Tier 2. The results for any EMDB entry are available in the validation tab of the EMDB entry page, for instance: https://www.ebi.ac.uk/emdb/EMD-11145
- Tier 3: successful metrics from Tier 2 are eventually included in the wwPDB validation pipeline, server and reports. The reports can be accessed from the "Download" button on Tier 2 entry page and a link inside "Additional validation information" on Tier 1 page. The reports (aimed at a wider audience, including editors and reviewers) are available from the wwPDB partner sites, for example: https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/zb/6zb5/6zb5_validation.pdf.gz
Software availability and installation
For local use, the Tier 1 version of the VA software can be obtained as part of a CCP-EM installation or by manual installation from PyPI. In both cases, there are some external dependencies that need to be installed if the corresponding validation metrics need to be calculated:
Funding
The work on the validation resources at EMDB is funded by the Wellcome Trust (grants 208398/Z/17/Z and 212977/Z/18/Z) and EMBL-EBI.
