X-ray validation reports added to PDB archive

X-ray validation reports added to PDB archive

Validation reports for all X-ray crystal structures released in the PDB archive are now publicly available. The reports are accessible from the following FTP sites:

The reports were added to the FTP archives as part of the March 19, 2014 update, adding ~56 GB of data. Files are organised in directories following the 2-character hash code format. For example, files for entry 1ABC will be found in directory /pdb/validation_reports/ab/1abc/. All files are compressed using gzip () compression.

Five files will be included in the directory for each entry:

  • Standard wwPDB validation report as a PDF file (e.g., 1abc_validation.pdf.gz)
  • Validation report containing all outliers as a PDF file (e.g., 1abc_full_validation.pdf.gz)
  • Summary quality graphic as a PNG image (e.g., 1abc_multipercentile_validation.png.gz)
  • Summary quality graphic as a SVG image (e.g., 1abc_multipercentile_validation.svg.gz)
  • Data file containing all diagnostics in machine-readable XML format (e.g., 1abc_validation.xml.gz)

Instructions for downloading data from the PDB archive .Ìý

The validation reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs.Ìý

The reports implement recommendations of a large group of  on validation of X-ray crystal structures and have been developed in the context of a larger initiative, the new , which was created to unify the annotation tools and practices used across all wwPDB deposition centers and for all common structure-determination methods.Ìý

The new X-ray structure-validation reports have been provided to depositors as part of the structure-annotation process . More recently,  was launched allowing crystallographers to generate reports on demand in order to check early, intermediate and near-final models and to help them to identify any potential problems that need addressing prior to structure analysis, publication and deposition.Ìý

Further information, including sample X-ray validation reports, . We welcome your feedback on the new validation reports. If you would like to send us your comments or questions, then please contact [email protected].Ìý