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
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: firstname.lastname@example.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
- 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
- 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
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!