[3dem] Tools for searching and analysing EMDB

[Ardan Patwardhan]

Dear all,

 

The Protein Data Bank in Europe (PDBe; pdbe.org) has introduced a number of
improvements to the web services it offers for searching and analysing EMDB:

 

Searching EMDB

We have made searching easier by implementing search filters that enable you
to rapidly narrow down search results. You can specify terms in a search
form (http://pdbe.org/emsearch), or browse the contents of the archive
(http://pdbe.org/embrowse). In line with our philosophy of agile development
we are conducting a survey on the usability and content of the filters -
http://www.surveymonkey.com/s/emdb_search_filters and welcome your
participation! 

 

Analysing EMDB

We introduced the "Visual analysis" pages, e.g.,
http://pdbe.org/emd-5357/analysis for EMDB entry EMD-5357,  last year as a
means of showing basic validation for all EMDB entries. We have now added
the following features to these pages:

               1) Volume plot - the enclosed map volume is plotted against
contour level. The recommended contour level is shown as a vertical line. If
the molecular weight of the sample was provided, the volume calculated from
it based on a conversion factor is shown as a horizontal line. In the ideal
case, the curve intersects the horizontal and vertical lines at the same
point.

               2) Fourier shell correlation curve - in cases where this has
been uploaded, e.g., http://pdbe.org/emd-5357/analysis.

               3) For each PDB model that has been fitted to the map we now
show a residue-based atom inclusion chart, e.g.,
http://pdbe.org/emd-2017/analysis. The rainbow scale from green to red
indicates the degree to which the residue is included in the map volume at
the recommended contour level (green symbolizes full inclusion).

               4) Currently segmentations are handled as mask files in EMDB.
For maps with deposited masks, we now show an overlay of the mask on the
map, e.g.,  http://pdbe.org/emd-1206/analysis

 

As always we are very keen to hear from the community so please feel free to
email comments and suggestions to emhelp at ebi.ac.uk!

 

Best Wishes

 

Ardan Patwardhan

The Protein Data Bank in Europe (PDBe; pdbe.org)

EMBL-EBI

Hinxton, Cambridge CB10 1SD, UK

 

Tel: +44 1223 492649

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