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.

• 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 correctly 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.

• 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.
• 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