Stand-alone wwPDB Validation Service

The wwPDB Validation Service (https://validate.wwpdb.org) is a web server that allows users to upload their structures and (optionally) experimental data and generate a wwPDB validation report. This server performs the same validation as you would observe during the deposition process. This service is designed to help you check your model and experimental files prior to deposition.

To create a validation account that allows you to use the server, please go to https://validate.wwpdb.org.

Important notes about the wwPDB Validation Service:

  • The wwPDB Validation Service now works for models/data of structures determined by X-ray crystallography, Nuclear Magnetic Resonance spectroscopy (NMR) and 3D Cryo Electron Microscopy (3DEM).
  • The wwPDB Validation Service and Validation Reports are relatively new, under active development and have some bugs and limitations.. We appreciate your feedback and suggestions for improvement - please mail these to: [email protected].
  • User guides describing the contents of the wwPDB validation reports, an FAQ, and example reports are available online
  • The validation reports produced by the stand-alone wwPDB Validation Service are preliminary reports for your information only. They are not official wwPDB validation reports (which contain more checks and information, in particular about sequences and ligands), and they should therefore not be submitted to journals. Once you have deposited your structure with the wwPDB, you will receive the official confidential wwPDB validation report from our biocuraton staff - this is the report that can be submitted to journals with your manuscripts.
  • The validation report produced by the wwPDB Validation Service is preliminary because currently no attempt is made to match (or have the user match) ligands to the wwPDB Chemical Components Dictionary. At a later stage, we will implement a "lite" version of the ligand module that we use in the new wwPDB biocuration system to make it possible (but not mandatory) for users to do this and thus get more information (e.g., about missing atoms and chirality violations in ligands). Because of this, currently only limited validation is made for ligands and occasionally incorrect chemical assignment is made when using Mogul to compare ligands against small molecule crystal structures.

Please keep in mind the following technical issues:

  • The server is essentially a scaled-down variant of the new wwPDB OneDep deposition system. This means that the first step is to create a "validation account". You will receive an email about where to go and can then proceed to upload a model and a data file. You can only run one validation job per account at a time. You will receive an e-mail when the calculations are done (or have failed or have been terminated; see below) - you can then go back to the server to see if your results files have been created (PDF report and XML file with exhaustive results).
  • Please note that the wwPDB Validation Service and OneDep system although related are entirely separate. The Validation ID cannot be used for deposition. Once you are satisfied that your structure is ready for deposition to the PDB you will need to start a new deposition at OneDep http://deposit.wwpdb.org.
  • You are welcome to reuse your "validation account" on the Validation Service for other models and data files as many times as you wish. Please note that we periodically delete accounts that have been inactive for over 3 months. If this happens then simply request a new account. You will also need to have more than one account if you validate structures from multiple methods (for instance X-ray and 3DEM).
  • The server runs on a load-balanced set of 2 web servers and 2 compute servers (2 x 16 CPUs, 2 x 128 GB RAM). In case of heavy server load, your job may take a while to complete. Most jobs finish in 5-10 minutes (~20 minutes for NMR ensembles), but jobs with huge models and/or data sets can take considerably longer.
  • Any validation run will be terminated automatically after it has used 2 hours of CPU time. This should allow 99% of the jobs to complete and prevent failing jobs from hanging and consuming compute resources. If your job is terminated, an e-mail is sent automatically to our technical staff who will look into the issue.
  • For X-ray structures, if there are multiple data sets in a mmCIF reflection file, only the first one will be used.
  • The more complete and compliant to standards your input files are, the more likely that the validation report will succeed. Some of the software packages in the pipeline still fail occasionally, and we are working with the authors of those packages to correct the problems.
  • Your files will be deleted two days after you last used the validation server, or you can delete them yourself at any time. We make every reasonable effort to keep your data confidential, but our technical staff may need access to them for debugging purposes (if you don't agree to that, simply delete your files). Use of the validation server is in no way connected to deposition and uploaded files cannot be directly transferred from the validation server to the deposition server.
  • You may compress your files using gzip or bzip2 prior to uploading them.