[3dem] EMAN2.9/SPHIRE1.4/SPARX has been released!

[Ludtke, Steven J.]

https://urldefense.com/v3/__http://eman2.org__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5VCJ6g4bw$ 

We are pleased to announce the release of EMAN2.9/SPHIRE1.4/SPARX. This announcement focuses on EMAN2, but as usual, SPHIRE and SPARX join EMAN2 in a combined distribution. If you install any of the three, you will have all 3.

The new tomography pipeline in EMAN2 has been significantly improved since its initial release, and other significant new tools have been added as well. Data compression is now a standard part of the package for both CryoEM and CryoET data processing pipelines, providing dramatic reductions in disk usage and transfer times with no reduction in quality. This is also the first release of EMAN2 to be based on Python3!

  *   Documentation: eman2.org<https://urldefense.com/v3/__http://eman2.org__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5VCJ6g4bw$ >
  *   For assistance: Google Group<https://urldefense.com/v3/__http://groups.google.com/group/eman2__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5XsWX6eyw$ >
  *   For confidential assistance or for users without Google access: email sludtke -at- bcm.edu<https://urldefense.com/v3/__http://bcm.edu__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5V4ReV6Tw$ >

 There are many changes and improvements throughout the system, summarized below:

  *   Numerous improvements for in-situ subtomogram averaging
     *   Full PPPT subtomogram averaging pipeline capable of near-atomic resolution
     *   Fully automated tilt series alignment/reconstruction with no need for fiducials (new options)
     *   New dedicated deep-learning tomography particle picker
     *   Simultaneous (visual) picking of multiple macromolecular species
  *   Data compression support for both CryoEM and CryoET
     *   Native HDF5 mechanism
     *   lossless or lossy with user-selectable bit count
     *   Files still readable by Chimera
     *   No quality/resolution loss
     *   Typical 10-20x project size reduction, dramatically improves disk I/O and network transfer
  *   Extensive work on e2boxer
     *   improved deep learning picker
     *   Fixed problems with reference-based and local pickers
     *   Added simple inline instructions
  *   Deep learning GMM for single particle variability studies (e2gmm.py, see arxiv paper, experimental)
  *   New local resolution and filtration based on mFSC (Penczek), for SPA and SPT (iterative)
  *   New visualization options for volume stacks
  *   Support for EER format & oversampling (counting-mode Falcon 4 images)
  *   Speed improvements for image I/O operations
  *   Better integration with Numpy and Jupyter with image object data sharing (advanced users)
  *   Python 3 based


--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke at bcm.edu<mailto:sludtke at bcm.edu>>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (https://urldefense.com/v3/__http://www.bcm.edu/biochem__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5UQReawBw$ <https://urldefense.com/v3/__http://www.bcm.edu/biochem__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5UQReawBw$ >)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<https://urldefense.com/v3/__http://cryoem.bcm.edu__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5UTTaB3gA$ >)
Co-Director CIBR Center                                    (https://urldefense.com/v3/__http://www.bcm.edu/research/cibr__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5V3gADksg$ <https://urldefense.com/v3/__http://www.bcm.edu/research/cibr__;!!Mih3wA!XeqQQEhOJGZ5AYruFbPlFPlnjcUgzOEnLz3rmL3YAoF_0lPoPvT7OY-_n5V3gADksg$ >)



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20210212/6f4a6795/attachment.html>