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Uppsala Electron Density Server (EDS) to be retired
After two decades of serving the scientific community, the Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) will be retired in 2018 (date t.b.a.). Much of its functionality will be provided by the PDB-entry pages of the Protein Data Bank in Europe (PDBe; http://pdbe.org/) at EMBL-EBI in Hinxton, UK. 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. 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.
What does this mean for users of the EDS website?
We recommend that users of the EDS website start using the PDBe website from now on to view and download electron-density maps. For a given PDB entry, say 1CBS, the PDBe entry page can be accessed with the URL http://pdbe.org/1cbs . Clicking on the link "3D Visualisation" in the right-hand panel brings up the LiteMol viewer. 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). A LiteMol cheat-sheet is available at http://www.ebi.ac.uk/pdbe/litemol . 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.
For 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:
• The 2mFo-DFc map (in CCP4 format): http://www.ebi.ac.uk/pdbe/coordinates/files/1cbs.ccp4
• The mFo-DFc map (in CCP4 format): http://www.ebi.ac.uk/pdbe/coordinates/files/1cbs_diff.ccp4
• The reflection file (in MTZ format): http://www.ebi.ac.uk/pdbe/coordinates/files/1cbs_map.mtz
Users may also be interested in a tutorial about model validation that covers the use of LiteMol and the PDBe website: http://www.ebi.ac.uk/pdbe/modval1 .
Note that the plots that you may use on the Uppsala EDS website, e.g. Ramachandran plots and real-space R-value versus residue plots, are not yet available. However, for every PDB entry there are wwPDB validation reports that cover much of the information you may be after (using 1CBS as an example again):
• The summary report (listing no more than five outlier for any criterion): http://www.ebi.ac.uk/pdbe/entry-files/download/1cbs_validation.pdf
• The full report (listing all outliers for all criteria): http://www.ebi.ac.uk/pdbe/entry-files/download/1cbs_full_validation.pdf
Figure 1. Detail of structure and electron-density maps near Trp B170 in entry 1QW9 (http://pdbe.org/1qw9), in the LiteMol viewer on the PDBe website.
Figure 2. Detail of structure and electron-density maps near Trp B170 in entry 1QW9. Maps downloaded from EDS (http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1qw9) and viewed in "O".
What does this mean for users of software such as Coot and Chimera, which retrieve map data from EDS?
We have contacted the developers of major software packages that do or may use data from the Uppsala EDS site, e.g. Coot and Chimera, to inform them of its upcoming retirement. Hopefully, future versions of these packages will retrieve their data from the PDBe site instead. 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 (http://www.ebi.ac.uk/pdbe/eds).
What does this mean for software developers who use EDS data?
Anyone who uses data from the Uppsala EDS site programmatically will have to switch to using the PDBe site. The URLs for map and reflection files as well as the wwPDB validation reports were already listed above. In addition, developers may be interested in the following (again, using 1CBS as an example):
• The XML file with wwPDB validation information for every PDB entry: http://www.ebi.ac.uk/pdbe/entry-files/download/1cbs_validation.xml
• The clean mmCIF file containing the structure: http://www.ebi.ac.uk/pdbe/entry-files/download/1cbs_updated.cif
Note that all metadata (incl. PDB "header" data, validation data, up-to-date SIFTS mappings to UniProt, etc.) for every entry is conveniently available through the PDBe API: http://pdbe.org/api . 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: http://wwwdev.ebi.ac.uk/pdbe/api/pdb/entry/electron_density_statistics/1cbs (this will return a JSON string for entry 1CBS).
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Figure 3. Structure and density maps for the retinoic-acid ligand in entry 1CBS (http://pdbe.org/1cbs), viewed in LiteMol on the PDBe website.
Figure 4. Structure and density maps for the retinoic-acid ligand in entry 1CBS, viewed in the AstexViewer on the EDS website (http://eds.bmc.uu.se/cgi-bin/eds/eds_astex.pl?infile=1cbs).