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Stand-alone wwPDB validation servers

The wwPDB partners will provide access to stand-alone versions of the various validation pipelines, allowing experimental structural biologists to validate their models prior to publication and deposition. At present, the wwPDB X-ray validation server is available; servers for validation of NMR en EM models will be made available at a later date.

Important notes about the wwPDB stand-alone X-ray validation server:

  • This version of the validation server is still in beta testing. We appreciate your feedback and suggestions for improvement - please mail these to: validation@mail.wwpdb.org

  • A user-guide describing the contents of the new wwPDB validation reports (PDFs), an FAQ, and example reports are available online

  • The validation reports produced by the stand-alone server are 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 wwPDB validation and annotation report from our annotation staff - this is the report that can be submitted to journals with your manuscripts.

Please keep in mind the following technical issues:

  • The server is essentially a scaled-down variant of the new wwPDB deposition system. This means that the first step is to create a "validation account", which can then be reused over and over. 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).

  • 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, but jobs with huge models and/or data sets can take considerably longer.

  • Any validation run will be killed 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 gets killed, a mail is sent automatically to our technical staff who will look into the issue.

  • At present we make no attempt 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 annotation 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).

  • If there are multiple data sets in a CIF reflection file, only the first one will be used.

  • The more "standard" your input files are, the more likely that the validation report will succeed. Some of the programs in the pipeline still fail occasionally, and we are working with the authors of those programs to try and fix 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.

  • Note that the server only handles X-ray structures at present and requires uploading of both a model (in PDB or mmCIF format) and a reflection file (with intensities or amplitudes, in mmCIF or MTZ format). You may compress your files using gzip or bzip2 prior to uploading them.

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

The wwPDB partners hope that you will find the validation server useful in your work!


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