[3dem] Improved EM-related resources at PDBe

[Gerard DVD Kleywegt]

Hi all,

The Protein Data Bank in Europe (PDBe; http://pdbe.org) continues to improve 
its services to the scientific community. As part of our recent website 
update, the EM resources at PDBe (http://pdbe.org/emdb) have been improved.

EMDB (http://emdatabank.org) contains over 1000 maps and is expected to grow 
5-10 fold over the next 10 years. The data held in EMDB form a treasure trove 
of information on the state of, and trends in, the 3DEM field. Examples of 
interesting information that can be mined from the archive are trends in the 
resolution obtained using different techniques and comparisons of the relative 
popularity of microscopes and software packages. A new service 
(http://pdbe.org/emstats) has been developed at PDBe to mine the database for 
such information and present the results as interactive charts. The charts are 
generated dynamically and represent the current state of the information in 
the database. The charts are active, i.e. when clicked, a query is sent to the 
database and the results are shown below the charts. Clearly, the current set 
of charts represents only a fraction of the interesting information that can 
be extracted from the database and we invite the 3DEM community as well as the 
wider structural biology community to engage with us in expanding this 
service.

Atlas pages for EMDB entries can now be accessed directly using URLs of the 
type: pdbe.org/emd-xxxx, where "xxxx" is the 4-digit numerical EMDB accession 
code. For example, http://pdbe.org/emd-1831 takes you to the entry "Pig 
Gastric H,K-ATPase with bound BeF and SCH28080" by Abe, Tani and Fujiyoshi.

The look and feel of the EMDB atlas pages (served at both EMDataBank sites, 
PDBe and RCSB) have also been improved - for instance, empty boxes are not 
shown so as to create a cleaner and more concise look and an enhanced version 
of the OpenAstexViewer can be accessed from an entry's visualisation page. The 
viewer can overlay fitted PDB models on maps (for an example, see 
http://pdbe.org/emd-1180) and use symmetry information to generate 
symmetry-related copies of models. (See also: 
http://www.emdatabank.org/improved_3d_viewing.html)

We hope that you will find the EM resources at PDBe useful. As always, we 
welcome constructive criticism, comments, suggestions, bug reports, etc. 
through the feedback button at the top of any PDBe web page.

--Gerard

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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard at ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin at ebi.ac.uk