New Publications

New open access articles about EMDataBank and EMDB access are now available online, in advance of publication in the upcoming January 2016 Nucleic Acids Research Database Issue.

Map Challenge FAQ

Below are compiled questions/answers regarding the map challenge that may be of interest to all of the participants.  We'll update this FAQ as needed.

Challenge Phase

1. Is the Cs listed in the target table (2.7) correct for the Apoferritin data?  No. There was an error in the script to generate the metadata requested for the challenge. The manufacturer specified Cs value for the Polara is 2.0 mm, but this has never been measured accurately for the instrument. In practice, this is an somewhat arbitrary fitting parameter that can be input during analysis of the raw data or refined during fitting. Followup question: What Cs do the defocus values provided in the particle stack refer to?  The provided defocus values assume Cs = 2.7. posted Nov 20, 2015, thanks to Niko Grigorieff for questions, and Chris Russo for answers

SDSC Gordon Info

Everyone who applied for SDSC Gordon compute time for the map challenge will receive an initial allocation of 22,000 service units per proposed target. Altogether 14 users plan to perform a total of 45 reconstructions. Some useful links:

Other things to be aware of:

SDSC Offers Supercomputer Resources; Map Challenge Submission Deadline Extended

Nov 9, 2015: We have two major announcements regarding the ongoing EMDataBank Map Challenge.

First, the San Diego Supercomputing Center (SDSC) is generously offering supercomputing resources to support the Map Challenge.  The resources, made available through an SDSC Director’s Discretionary Award, include 1 Million core-hours on SDSC Gordon and 20TB of sandbox data storage on Gordon’s parallel file system Data Oasis.


Map Challenge

The Blind Assessment Phase is now open (Nov 2016-midFeb 2017).  Please visit the map challenge page for more details.

Model Challenge

The Assessment Phase for the 2015/2016 Model Challenge is now open. Please visit the model challenge page for more details.


 Three-dimensional Electron Microscopy (3DEM) is becoming a key experimental method in Structural Biology. Recent advances in image acquisition and processing are yielding more structures determined at near-atomic resolution, as well as a wide range of macromolecular complexes and subcellular architectures determined at lower resolution.


A major goal of the EMDataBank team is to work with the 3DEM community to establish data validation methods that can be used in the structure determination process, define key indicators of a well-determined structure that should accompany every structure deposition, and implement appropriate validation procedures into a 3DEM validation pipeline. Following recommendations of the EM Validation Task Force (Henderson et al 2012), we are hosting new benchmark challenges here, with aim to stimulate further community discussions about validation procedures for 3DEM maps and map-derived models. Prior community-organized 3DEM challenge activities have included a Particle Picking Challenge (Zhu et al 2004),  CryoEM Modeling Challenge (Ludtke et al 2012), and CTF Challenge (Marabini et al 2015).

EMDataBank Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to

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