Validation Server

Validation Tutorial | Possible Format Problems

Generate Validation Reports to monitor improvements made to your structural model.

Option 1: wwPDB Validation Server for X-ray

These reports are not the official wwPDB validation reports submitted to journals, but are useful in the preparation of your depositions.

The server is available at

Option 2: Validation Report with Detailed Geometry (Plain Text)

Check the format consistency of coordinates (PRECHECK) and run geometric and experimental data checks (VALIDATION) outside of the deposition pipeline. These checks can be done independently by the user.

The report produced by this option includes close contacts, bond deviations, and covalent bond distances and angles.


Option 3: Validation Report with High-level Summary (PDF)

Upload your data files to generate a summary PDF that contains high-level geometric and experimental checking results without listing the detailed geometry. This unofficial report is similar to the PDF reports generated for journal submission during deposition.

Upload coordinate file Select file type: PDB

Upload structure factor file (X-ray only)

Use SF-Tool to convert files to mmCIF or mtz format

Select file type: mmCIF
Select SF Validation Program(s) to include in report:

If your refinement program is not listed then select
        PHENIX X-Ray
        PHENIX Neutron Diffraction
        PHENIX Hybrid X-Ray/Neutron Diffraction

When you are ready, use the wwPDB Deposition System (X-ray only) to deposit your entry. A Validation Report PDF that can be shared with journals will be sent to you after processing.

Question, Comments, and suggestions should be sent to