Validation Report PDFs
wwPDB members currently provide depositors with detailed reports that include the results of geometric and experimental data checking as part of the structure annotation process. These documents are available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.
As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site (Example reports: RCSB PDB | PDBe | PDBj).
PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process.
The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures and the wwPDB Common Deposition & Annotation Tool.
Summary Validation Report FAQ
Question 1: What information will be made available about the structure before the full coordinate file is released?
Similar to the manuscript submission process (where information is secure until the paper is published), only limited information is made available for the public prior to release of the coordinates (see also Question 2).
The summary validation reports sent to authors for inclusion with peer review include the results of geometry checks, structure factor validation, and ligand validation. Coordinates are not part of the validation report.
Requiring validation report PDFs has not had an impact on the number of submissions to IUCr journals.
Question 2: What is the timing on making information about the submission publicly available? What is the timing for releasing the coordinates, etc.?
These summary validation reports are generated as part of the current data deposition and processing pipeline, and do not change any timings.
When structures are deposited, the author list, entry title, and release status (along with the pre-release sequence, if selected) are made publicly available with the next weekly PDB update. The author list and entry title may be suppressed upon request.
Once the PDB entry is finalized and approved by the authors, data can be released as close to the publication date as our update procedures allow.
Question 3: How much control do authors have over the release of information?
Authors maintain complete control over the submission of the validation report PDF to the journal, and determine the entry's release status at the time of deposition.