EMAN 2.1 beta-2

Release Date



This the second beta release, a minor update to beta1. All of the major problems with the alpha releases have been fixed, and this release should be a fully usable replacement for EMAN2.0. We now strongly encourage ALL users to migrate. There are many many advantages to EMAN2.1 over EMAN2.0 (I was tempted to call it 3.0). Dropping BDB in favor of (Chimera compatible) HDF5 files and text files (JSON format) has made the whole package much easier and more stable.


Important performance note: EMAN binaries are compiled for maximum compatibility, not performance. On a modern Intel processor, the 64 bit binary may run 30-40% slower than the exact same version compiled from source with ENABLE_OPTIMIZE_MACHINE. Using the 32 bit Windows binaries on the exact same computer is over 60% slower. That is, the same refinement may run up to 2.5x faster on linux than using the 32 bit windows binaries. The windows builds are provided mainly for interactive programs, not large scale refinement runs.

Windows Users - The installer currently claims to be 2.06 when you run it. Please ignore this. After installing, run e2version.py and you will see the actual version information.

Note that current linux binaries were compiled for maximal compatibility. A custom compile from source on a modern Xeon can produce executables 30-40% faster than the current binaries.

Version changes

Changes since 2.1beta1:

  • e2refine_easy runs would crash after completing 1 iteration due to a missing dependency. This has been fixed.
  • when importing data to a project, it would include the folder name containing the micrographs before importing, causing some problems with tutorials. There is now a new checkbox to permit this in special cases only.
  • Other minor bugfixes

Changes since 2.1alpha1:

  • e2refine_easy much more efficient than EMAN2.0x, and produces gold-standard FSCs on the fly (~20x faster than Relion in testing, that's times, not percent)
  • e2refine_easy automatically selects almost all parameters
  • significant improvements to refinement reports
  • tiltboxer, RCT and tilt-validation should all be working now
  • evalparticles fixed
  • Full support for EMAN2 -> Relion, Relion -> EMAN2 and EMAN2 -> Frealign (more coming)
  • Experimental support for direct detector movie-mode processing
  • e2projectupdate21 to convert EMAN2.0 projects to 2.1
  • MPI support has been completely revamped for more efficient cluster computing
  • Volume series support in file viewer
  • Dramatically expanded single particle tomography (subtomogram averaging)
  • Revamped CTF fitting, including astigmatism support

Major Changes since 2.0x:

  • BDB system retired in all e2* programs (remains for backwards compatibility and SPARX)
  • Images stored in (Chimera compatible) HDF5 files by default, with metadata stored in human readable .json files.
  • New faster and more flexible file browser
  • Better tools for handling large projects
  • New multi-model 3-D viewer with slices and volume rendering
  • Windows remember where you put them

Download EMAN 2.1 beta-2

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