[3dem] ANNOUNCING EMAN2.1 (beta3) ... and a couple of other things

Steven Ludtke sludtke at bcm.edu
Fri Jun 13 10:16:05 PDT 2014

I decided to group three related announcements into a single message to limit the damage to people's inboxes :^)

First, a request to the community. The R01 grant supporting EMAN maintenance and development is going in for renewal in three weeks. I have a brief survey set up here (hopefully you don't have to type that URL by hand):


If you've ever used EMAN, I'd greatly appreciate it if you could take a couple of minutes to fill it out. It really isn't very long.

Second, since we haven't managed to host our big week-long workshop in a couple of years due to site/timing issues, we've started running (mostly) weekly live telecast tutorials on a range of topics. These are then archived as informal video tutorials. The first of these, dubbed:

EMAN2.1 - One hour to subnanometer resolution (on a laptop)

is available online via the EMAN wiki http://blake.bcm.edu/emanwiki/EMAN2/VideoTutorials and via my (sludtke42) YouTube channel.

Finally, after over a year of development, we are very pleased to announce the availability of EMAN2.1 (beta3). 


While we haven't quite put the "release" moniker on it yet, the beta3 is very stable and ready for day-to-day use.  Major improvements since EMAN2.0x include:

* Retirement of the "BDB" system which drove so many users crazy
  * All images are now stored by default as flat HDF files (chimera compatible)
  * Metadata is stored in human-readable JSON files, which can be seamlessly copied between projects
  * Easy e2projectupdate21 script to move from EMAN 2.0

* e2refine-easy
  * True Gold-Standard FSCs
  * Automatic FSC-based map filtration and masking
  * Automatic selection of almost all refinement parameters based on your data and built-in heuristics
  * Much faster due to automatic parameter optimization (typically 2-10x)
  * Generates full web-based refinement report including resolution plots, updated live during refinement

* Intersoftware compatibility
  * Convert EMAN2 projects in one step for cross-testing in Relion and/or Frealign
  * One-step Relion project conversion to EMAN2
  * EMX support (this is the future !)

* New graphical tools including multi-model 3-D visualization with sequence animation, Slices and annotation

* Revamped MPI support for compatibility with more clusters and interoperability with (co-distributed) SPARX

* A full suite of Single Particle Tomography (subtomogram averaging) routines, with a wide variety of available methods and GUI tools

* Improvements to file format support, including compressed TIFFs (often used with K2 movies), DM4, Falcon and others

If you are an EMAN2.0 user, I strongly encourage you to take the leap and upgrade now. For users of other software, we are trying very hard to make it easy to move between packages for comparative purposes.

We have done a number of validation tests among software now, and for "good" data sets, you can achieve virtually identical results using Frealign, Relion and EMAN2 (and almost certainly others). However, for heterogeneous or flexible molecules, you will find differences, making cross comparisons among software a valuable test in validating your results, or at least in determining how far you can reasonably trust them.


Steven Ludtke, Ph.D.
Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)
Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)
Co-Director CIBR Center                          (www.bcm.edu/research/cibr)
Baylor College of Medicine                             
sludtke at bcm.edu

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