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Protein Data Bank in Europe : PDBe new service links

As of mid January 2009 the Macromolecular Structure database group (MSD) has been renamed to the Protein Data Bank in Europe (PDBe) to highlight our close partnership with the wwPDB. Although we are retaining MSD services for a number of months, users of our services are advised to change links to our new resources. This document describes in details the changes required.

Services at the PDBe

Our services are being migrated to the new URL's for the PDBe. We will maintain old services for a short while to allows people to have continuity in their research and finally redirect old URL to the new PDBe URL's. Please change any links to our services using these examples:

Atlas pages at PDBe

You should refer to atlas pages at this link (the ID is in the path), note that the ligands page (for example) can be referenced directly by changing the "summary" at the end of the URL to "ligands". This resource will handle the following :

  • Atlas pages
  • Fail over to OCA
  • Redirect to pdbStatus for unreleased entries
  • Redirection for obsoleted entries
  • Error page for undefined ID.

Example for atlas pages

http://www.ebi.ac.uk/pdbe-srv/view/entry/????/summary.html
http://www.ebi.ac.uk/pdbe-srv/view/entry/1mbd/summary.html

As an interim measure the following (old) link to atlas pages has been redirected to the new atlas pages. Please CHANGE all atlas pages links to the above URLs and do not use the following as it will be dropped as we drop all msd services in about 4-6 months.

Example for temporary atlas redirect

http://www.ebi.ac.uk/msd-srv/atlas?page=summary&id=1mbd
(wwwdev URL exists for testing)

Viewer at PDBe

The viewer is opened using the following link. This link will open the viewer and render in the default "nice" simple view for the deposited entry

Example for entry rendering

http://www.ebi.ac.uk/pdbe-srv/view/entry/????/viewer
http://www.ebi.ac.uk/pdbe-srv/view/entry/1mbd/viewer
(wwwdev URL exists for testing)

The viewer is opened to render a particular assembly using the following URL, the second number is the assembly. The first number is the model number.

Example for assembly rendering

http://www.ebi.ac.uk/pdbe-srv/view/entry/????:1,1/viewer
http://www.ebi.ac.uk/pdbe-srv/view/entry/4hhb:1,1/viewer

Viewer with multiple parameters (maintaining the original version)

For compatibility for external resources links the ViewerServlet has been re-written and is now accessible as

Example for entry rendering

http://wwwdev.ebi.ac.uk/pdbe-as/PDBeViewer/ViewerServlet?id=????
http://wwwdev.ebi.ac.uk/pdbe-as/PDBeViewer/ViewerServlet?id=1mbd

This servlet supports following parameters and runs the viewer directly with the required parameters. This resource will be maintained and include additional parameters as required to support service requests.

Simple option : produces the "nice" view of a molecule

  • id ( id=1abc )

Alternatively : allows the display to tuned : notice the nice view is not the default

  • selected ( selected=1abc?selected=2abc... )
  • unselected ( unselected=1abc?unselected=2abc... )
  • view ( view=defaultView / view=defaultViewStick )
  • map ( map=map1?map=map2 )
  • attributes ( attributes=on )
  • script ( script=display spheres on all; )
Reading a PDB file from the PDB

You can get an uncompressed PDB file from this URL. This URL is a query of the new database schema and returns coordinates as if it is a flat file.

Example getting a PDB file

http://www.ebi.ac.uk/pdbe-srv/view/files/????.pdb
http://www.ebi.ac.uk/pdbe-srv/view/files/1mbd.pdb
(wwwdev exists for testing)

The old flat file directory is being maintained BUT NOT INCREMENTED. Do not use this directory, please refer to the above URL to get structure coordinates.


Document mantained by: Gaurav Sahni
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