2017-06-28 : 4898 EMDB map entries, 1652 PDB coordinate entries PDBe | RCSB    

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voxel fix

Remediated Maps Available in Beta

June 2010: The EmDataBank.org team is nearing completion of a major project to improve uniformity, viewability and useability of the 730+ map volumes in the EMDB that are currently available for download. Please read on to learn more about this project, and how to access the remediated maps.

What changes have we made to the maps?
First, parameters in the CCP4 format map headers have been updated to reflect depositor-provided voxel sizes, enabling viewing and analyses of the maps at the correct physical scale. In the example at right, hepatitis B virus (EMD-1403) is shown as viewed in the graphics program UCSF Chimera before (grey, bottom right) and after voxel size remediation (radial rainbow color). Second, maps have been repositioned to superimpose over corresponding fitted PDB models, enabling evaluation of fit. Third, map density statistical values stored in map headers (min, max, avg, rmsd) have been updated/corrected to assist with identification of suitable contour levels for viewing. In a few cases map hand was also corrected or protein density was made positive.

Why are we remediating the 3D map volumes?
Processes used until recently to convert deposited EM maps from various formats to the distributed CCP4 format preserved map dimensions and density values but did not always retain scale or position information. Restoring the correct scale and position facilitates analyses such as evaluating model fit, viewing related maps, and making volume measurements. Improving uniformity of EMDB maps also enables systematic analyses to be performed across the entire database.

Where are the remediated maps?
[September 2010 update: updated maps are currently accessible via our public search and ftp services].

Questions, comments, suggestions?
We welcome your feedback on the beta services and remediated maps. Please contact us at help@emdatabank.org.