ChangeLog

We suggest subscribing to or searching the Google Group when you have questions. We have resumed updating the ChangeLog here as well as of version 2.91

Note the new version numbering scheme. Every time someone triggers a new binary snapshot to be built (also available via conda install), the version number is now automatically incremented.

This includes only significant changes. See Github for the complete set of changes/patches.

Date

Version/Patch

Change

2023/03/09

2.99.47

Version marked as official release

2023/03/04

2.99.47

Fixed problems with e2spt_refinemulti_new and compatibility with e2spt_refine_new with generated classes. Also some parallelism fixes.

2023/02/25

2.99.46

Added e2spa_refine to e2projectmanager (new single particle refinement tool). Removed some historical remnants. Changed e2spt_boxer_convnet negative example selection to work on Macs.

2023/02/23

2.99.45

Box file import/export options added to e2procjson. e2json2list moved from examples to programs (used to convert old-style SPT refinement files to new-style files). Some final pre-release fixes for e2gmm GUI, including making set -> lst file generation work properly.

2023/02/16

2.99.44

Changes related to binary build system in preparation for release

2023/02/16

2.99.42

Minor tweaks to e2gmm GUI. Bugfix for e2proc2d. Linear extraction from tomograms.

2023/02/14

2.99.41

e2gmm_refine orientation refinement improvements (not part of e2gmm GUI). Various improvements to the older tomogram manipulation pipeline (see GitHub for details)

2023/01/30

2.99.40

Ability to read hacked PDB files with >9999 residues. First version of GMM based orientation refinement. Contributed improvements to e2helixboxer. e2gmm_refine_point improvements to support large numbers of particles

2022/12/06

2.99.39

Contour plots added to 2-D scatter plot display. Minor e2gmm GUI improvements. Histograms in e2proctxt. even/odd splitting for subparticle refinement. Many minor bugfixes and improvements (see GitHub)

2022/11/13

2.99.38

Fix for rendering on older OpenGL systems

2022/11/12

2.99.37

Fixes for new point classification schemes in e2gmm GUI

2022/11/10

2.99.36

New classification schemes and better set manipulation introduced in e2gmm GUI. Fixes for get_image_count

2022/10/29

2.99.35

Added splitters to e2spt_boxer GUI so the relative size of the X/Y/Z slices can be adjusted. Other minor fixes.Chunk mode in e2gmm and e2gmm_refine_point to handle large data sets (50k+ particles).

2022/10/07

2.99.34

New bispectral invariant type with more completeness for particle classification. e2gmm now generates some negative density gaussians to help better characterize motions. Significant changes to e2gmm GUI, not stable yet

2022/08/18

2.99.33

First fully functional support for subtomograms in e2gmm_refine_point and e2gmm GUI. e2display --plot3d fixes. Initial try at adding splitter to adjust sizes in e2spt_boxer. e2gmm GUI now uses e2gmm_refine_point instead of e2gmm_refine. New approach eliminates Gaussian width, and changes gradient computation.

2022/08/05

49e4407

Fix some issues with compressed HDF files when sigma is specified. Fix some issues with helical symmetry use. New "helix filter" processor added.

2022/07/09

8dcb292

Changes to improve new compressed HDF format, and extend to other formats (bit reduction in formats not supporting actual compression).

2022/05/19

51bc852

Support for SerialEM style HDF files. New comparator looking for FRC/FSC threshold resolution. BDB file storage support removed from system (use 2.91 release if you need to read old BDB files)

2022/04/20

1d98c6a

Most recent fixes for EER format reading. Should support latest version of EER files

2022/03/01

8dd9b91

Add support for new-style refinement programs to e2gmm GUI

2022/01/27

377e65e

Binary compilation of "compatibility" EMAN2 builds now targets Haswell (ca 2014) generation processors

2021/12/12

a142fb2

Better masking options for new spt multimodel refinement. Option to make CTF corrected tomograms. e2evalimage improvements.

2021/10/29

d7aaeb7

.lst file bug, not providing image source info in header. Better rendering of image stacks in e2filtertool. Threadsafety for .lst file reading. New orthogonal slice display option for volumes.

2021/09/12

b337d0f

math.fft.peak processor improved for NPC membrane removal. Audio support in e2fftsynth demo (for teaching Fourier transforms). SPHIRE fixes in Python3 conversion. Remove --force options from many single particle refinement programs.

2021/07/22

f256807

New LST reader supporting new format ddecision. Early version of e2gmm GUI. Improve interaction with .mdoc files. New method for making various improvements and fixes for SPHIRE related to Python 3.

2021/03/08

2.91

Version release

Older changes. Note that we didn't use a changelog on the Wiki for about 12 years, relying only on the discussion group: 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.

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 :

EMAN2.0RC2 Released

EMAN2/ChangeLog (last edited 2023-03-11 01:10:54 by SteveLudtke)