Finding detail in the (EM) data

Image to highlight the EM search improvements at PDBe
05 June 2018

Cryo-electron microscopy (cryoEM) is a field that has made dramatic advances in recent years. This has resulted in many more PDB models, derived directly from electron microscopy data, being released in recent years, therefore it is increasingly important to provide tools for searching and analysing this data.

Due to the increase in available structures and the importance of accessing this data for the biological research community, we have been working hard to make EM models and their related data more searchable for PDBe users. We have cleaned up a large number of EM-specific fields and made many of these searchable, something we’ve enabled in our recent search update.

Search terms that have been added for electron microscopy include many describing the data collection, for instance the microscope and electron detector models (and mode used), the energy filter and the grid type. There are also a number of search terms defining the image processing procedures, including the software used at , number of particles and the resolution.

Example of EM fields available in the new PDBe search

These updates allow you to do much more complex searches of EM entries in the PDB. For example, you can search for structures solved to better than 5Å resolution, on a Falcon II detector with a C2 aperture of between 60 to 70mm. Or alternatively you may be interested in investigating the structures solved using a detector in counting mode, that have helical symmetry.

We hope that these changes will make it much easier for users from the whole scientific community to find electron microscopy structures of interest to them. If you have any comments or questions about our latest website improvements then we would love to hear from you. Either hit the feedback button on any PDBe webpage or email us at