|
Size: 713
Comment:
|
Size: 3236
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 6: | Line 6: |
* 04/28/2010 |
* 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. * 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. |
| Line 10: | Line 31: |
| * 04/22/2010 | * 4/22/2010 |
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.
- 7/19/2010
- 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.
- 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