EMAN 2.04

Release Date



This is a minor update of EMAN 2.03, including bug fixes and some feature enhancements

The EMAN2 binary and source downloads also include SPARX !

Please follow the installation instructions at:



Documentation is provided through the EMAN2 Wiki

Windows users - Please note that while we do our best to periodically test the windows release to make sure it's still functioning, it is far less well-tested than the linux/Mac releases. Please report any problems you encounter.

Mac users, we do not support 10.5 since there are a number of issues with OS provided dependencies not working as they should.

Linux users - Linux x86 is for 32 bit Linux. Linux x86_64 is for 64 bit Linux. use command 'uname -i' to determine whether your Linux is 32 bit or 64 bit if you are not aware. The GCC4 binaries are new as of 4/2010, and provide a significant performance boost. It needs glibc version at least 2.5. You can check your system's glibc version by using command '/sbin/ldconfig -V'. Warning:We disabled the fftw cache for eman2.daily.linux64.tar.bz2 since it causes segfault on some size of image. That means it runs considerably slow compare to the gcc4 version. So please use the gcc4 version as long as your system supports.

NOTE: There was a fftw library issue with EMAN2 Linux binary release, which is fixed in current daily release. If you see segmentation fault in e2classaverage.py, please use daily release.

If you see following error message when your run EMAN2 GUI program, please remove the Qt libraries (rm -rf libQt*.so) from your EMAN2/lib directory:

"Cannot mix incompatible Qt library (version 0x407**) with this library. (version 0x40703)"

Version changes

This version includes a substantial number of new features over the 2.03 release (though all have been available through the nightly snapshots). Major improvements include:

  • New e2filtertool.py program for interactive filtering and image processing of both 2-D and 3-D data
  • New e2evalimage.py program for interactive power spectrum analysis of raw (unboxed) CCD frames and scanned micrographs. Provides a variety of tools for subregion selection and basic CTF analysis. Designed for interactive use on the microscope during data collection, or to rapidly screen sets of images for quality.
  • New program examples/mergeproject.py which will take 2 projects and merge them into a single new project. For large projects with data in multiple groups, permits the groups to be processed independently, then merged together at some point for a large-scale refinement.
  • New processor 'math.simulatectf', which in conjunction with e2filtertool.py can be used to prepare very realistic simulated particle images
  • Improvements for support for icosahedral structures. Better tools now provided for moving between the various symmetry axis conventions.
  • e2ctf.py now shows a subset of the particle images associated with each data set
  • Color display of Fourier phases has been fixed.
  • MPI parallelism improvements, including experimental new option for disabling image caching for clusters with distributed filesystems like Lustre.

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