ChangeLog

This is a list of important changes by date. Only major changes will be listed here.

Note that if using binary versions, most reported changes will not appear in binary snapshots until ~5pm (Houston time) 1 day AFTER the date shown below.

• 8/18/2010
  • Fixed serious problem when probing values in the left half of the FFT display in 2-D images. Was not displaying the correct value. Note that there is still a ~1 pixel shift in some cases when probing. Look at the coordinates when using this feature. We are working on a new version of all of the display widgets.
• 8/10/2010
  • fixed significant bug in creation of virtual stacks with the 'e2bdb.py --makevstack' command
• 7/21/2010
  • More thorough fix for FFT rendering, though there are still a few issues.
• 7/20/2010
  • Note that the message saying we temporarily disabled RC3 downloads due to a potential CTF issue was resolved. It was user-error, not an actual bug. Everything is working fine.
  • Fixed color rendering of FFTs
  • Investigating issue related to incorrect phase-flipping if oversampling is used during fitting. (update : seems ok, must be a problem elsewhere)

EMAN2.0 RC3 Released

Important Note We recently discovered (and fixed) the cause of a serious problem in the 3-D reconstruction algorithm. If you did a 3-D reconstruction with the keep= option set to a value less than 1 (or used the sigma keep option), you would sometimes (but not always) get a streaked or blurred looking 3-D reconstruction. This was due to a very subtle bug in the 3-D reconstruction algorithm which is now fixed. If you ran into this problem, PLEASE rerun your refinements with this new version. They should be much improved. Several other significant enhancements have also been made. For users upgrading from an earlier version, here are some suggested things to try with projects you previously refined with an earlier version of EMAN2 :

• Try running a few more rounds of refinements. A number of subtle changes may have a positive impact on your results.
• Rerun the 'structure factor determination' step in the workflow. There is a new algorithm which extends the structure factor closer to the origin and improves results at higher resolutions. You should NOT need to rerun CTF determination, but recomputing the structure factor should improve results.
• If you are using the ctf.auto averager, note that it no longer includes Wiener filtration which is now supported as anisotropic Wiener filtration in 3-D. You can still generate Wiener filtered class-averages if you like using the ctfw.auto averager.
• There is now a wiener-fourier reconstructor in addition to the 'fourier' reconstructor. In most structures the effects may not be very significant, but it may be a good idea to switch. You can still use setsf and lowpass filter and get the benefits of the anisotropy of the Wiener filter.

Changes:

• 7/19/2010
  • Improved --twostage option, so it better distributes the first-stage classification references. This option provides dramatic refinement speedups.
• 7/15/2010
  • Threaded parallelism is now working !!! If all you want to do is use multiple cores on your local machine, all you have to do is put "thread:4" in the 'Parallel" box, or equivalently specify --parallel=thread:4 on the command line. No clients, no servers, etc.
• 7/9/2010
  • Fix for the parallelism client (e2parallel.py dcclient) gradually using more and more memory when running long jobs in parallel.
• 7/8/2010
  • Averager ctf.auto now does not include a Wiener filter. ctfw.auto was added to include this. Both averagers now store SNR info to be used in 3-D reconstruction.
  • Fixed another issue with 3-D reconstruction with the lowmem option.
  • New wiener_fourier reconstructor added. Works in conjunction with the improved ctf.auto averager to produce correct, anisotropically Wiener filtered 3-D reconstructions !
• 7/7/2010

  • Finally fixed bug producing strange looking reconstructions with keep<1 in 3-d reconstruction. If you were seeing streaked or stretched looking reconstructions, this should take care of it. This bug has been around for the last ~8 months or so. If you were having serious problems getting a good model from EMAN2 over that time period, please try again !

• 6/25/2010
  • CTF structure factor determination now extends almost to origin, significantly, now including the sharp peak near the origin. Remains to be seen if this will be a significant improvement or make some things worse. It will arguably improve the appearance of structures when setsf is used.
  • Circular mask in class-averages is now a soft Gaussian varying with box-size. This prevents sharp edge effects on the mask.
  • Particularly for structures with high c or d symmetry, may consider using the 'perturb' option on the eman orientgen to reduce problems with 'stripes' appearing in exact side views. (note this is now the default in RC3)

EMAN2.0RC2 Released

• 5/20/2010
  • fixed problem causing e2refine2d.py to crash
  • fixed 'prefilt' option (PS match ref in workflow). Was not working properly and even when disabled was causing some problems.
• 5/19/2010
  • Added --check option to e2bdb.py for verifying databases. Can check for some possible database internal inconsistencies
• 4/28/2010
  • Fixed long standing bug with remote display of single images using VNC or NX (www.nomachine.com). Power spectra and individual images should now display correctly.
  • New --automask option on e2refine2d.py and e2classaverage.py will help with centering negative stain data (and maybe cryo data that doesn't center well)
  • New mask.auto2d filter, similar to mask.auto3d
• 4/22/2010
  • Convergence plot was being improperly calculated, giving the impression of low resolution. Corrected for new e2refine runs. Old runs can be updated with examples/redo_convergence.py in a project directory