Questions, requests, comments or other feedback? The API will also provide the kind of summary information that is currently listed on EDS entry pages (and also in the entries' ".sfdat" files) - this functionality is currently in development and can be tested here: (this will return a JSON string for entry 1CBS). PDB "header" data, validation data, up-to-date SIFTS mappings to UniProt, etc.) for every entry is conveniently available through the PDBe API. The clean mmCIF file containing the structure:.The XML file with wwPDB validation information for every PDB entry:.In addition, developers may be interested in the following (again, using 1CBS as an example): The URLs for map and reflection files as well as the wwPDB validation reports were already listed above.
What does this mean for software developers who use EDS data?Īnyone who uses data from the Uppsala EDS site programmatically will have to switch to using the PDBe site. If, after the shutdown of EDS, you should encounter problems that you suspect might be due to the retirement of EDS, please contact the developers of the software package you are using and point them to this page ( ). Hopefully, future versions of these packages will retrieve their data from the PDBe site instead. Coot and Chimera, to inform them of its upcoming retirement.
We have contacted the developers of major software packages that do or may use data from the Uppsala EDS site, e.g. What does this mean for users of software such as Coot and Chimera, which retrieve map data from EDS? Maps downloaded from EDS ( ) and viewed in "O". Detail of structure and electron-density maps near Trp B170 in entry 1QW9. Detail of structure and electron-density maps near Trp B170 in entry 1QW9 ( ), in the LiteMol viewer on the PDBe website.įigure 2.
Users may also be interested in a tutorial about model validation that covers the use of LiteMol and the PDBe website.
From the entry page, clicking on any ligand will take you to a separate page that shows information about the ligand and its interactions and a panel with LiteMol showing the ligand and its neighbours with the density maps.įor users who want to view the maps off-line in a molecular graphics program, the following files are available for download (for X-ray crystal structures), using PDB entry 1CBS as an example again: For X-ray crystal structures (and EM structures) for which there is a map available, clicking on any atom suffices to show the map(s). Clicking on the link "3D Visualisation" in the right-hand panel brings up the LiteMol viewer. For a given PDB entry, say 1CBS, the PDBe entry page can be accessed with the URL. We recommend that users of the EDS website start using the PDBe website from now on to view and download electron-density maps. What does this mean for users of the EDS website? Other advantages are that PDBe provides a modern 3D viewer (LiteMol), that its PDB-entry pages contain a rich variety of added-value information and links, and that maps for new and updated PDB entries will become available at the same time as the entries themselves. Moreover, since the EDS software has not been updated since 2009, the quality and quantity of the electron-density maps provided by PDBe considerably exceeds that of the Uppsala site. Much of its functionality will be provided by the PDB-entry pages of the Protein Data Bank in Europe (PDBe ) at EMBL-EBI in Hinxton, UK. After two decades of serving the scientific community, the Uppsala Electron Density Server (EDS ) will be retired in 2018 (date t.b.a.).