[3dem] Announcing EMAN2.31/SPHIRE1.3/SPARX

Sat Oct 5 08:00:25 PDT 2019

Hi,

I would like to clarify that my group no longer participates in the SPHIRE project.

While SPHIRE remains largely based on the original SPARX code written by my group, the recently announced release takes multiple liberties with the original methodologies implemented in SPARX and compromise reliability of the outcome.
I recommended to exercise caution while using the new release of SPHIRE.
My original code remains available in SPARX.

Sincerely,

Pawel A. Penczek, Ph.D.
Professor
Department of Biochemistry and Molecular Biology
The University of Texas - McGovern Medical School
MSB 6.220
6431 Fannin
Houston, TX 77030
USA

phone: 713-500-5416
fax: 713-500-6297
pawel.a.penczek at uth.tmc.edu
http://www.uth.tmc.edu/bmb/faculty/pawel-penczek.html

________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Ludtke, Steven J. <sludtke at bcm.edu>
Sent: Friday, October 4, 2019 7:22 AM
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Announcing EMAN2.31/SPHIRE1.3/SPARX

**** EXTERNAL EMAIL ****

We are pleased to announce a new release of the joint distribution of EMAN2/SPHIRE/SPARX. This represents the final release before we transition to Python 3 (the end of the year when Python2 becomes deprecated).

see either:
http://eman2.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__eman2.org&d=DwMGaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=msFqnaSgAGSIZpJQlaQ4dHlGx98f2jE8HwKZZJX9a9s&s=oYsHCzD7D2aOhOuw692lWdtes3NKyrNlWIBXaoH6_9U&e=>
or
http://sphire.mpg.de/wiki/doku.php?id=downloads:sphire_1_3<https://urldefense.proofpoint.com/v2/url?u=http-3A__sphire.mpg.de_wiki_doku.php-3Fid-3Ddownloads-3Asphire-5F1-5F3&d=DwMGaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=msFqnaSgAGSIZpJQlaQ4dHlGx98f2jE8HwKZZJX9a9s&s=kz7L_nPAq4H5y4rtoUmA2wmcsWlvgx0lcLORny9O4oc&e=>

As always, all 3 software packages are part of a single installation. Each package uses a unique command prefix:

  *   EMAN2: e2
  *   SPHIRE: sp
  *   SPARX: sx

Version changes

EMAN2 major changes:

  *   PPPT (per particle per tilt) Subtomogram averaging:
     *   Automatic CTF based handedness checking for tomograms
     *   focused refinement https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_more#Focused_refinement<https://urldefense.proofpoint.com/v2/url?u=https-3A__blake.bcm.edu_emanwiki_EMAN2_e2tomo-5Fmore-23Focused-5Frefinement&d=DwMGaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=msFqnaSgAGSIZpJQlaQ4dHlGx98f2jE8HwKZZJX9a9s&s=To35DVeFFjZapRFRyf0EhtOY4Uykmh1HqdWzFJyzff8&e=>
     *   better parallelism
     *   improved tilt series alignment (resolution improvement)

  *   General changes:
     *   New browser options for display of stacks of 3-D volumes
     *   RCTboxer works properly again
     *   fixed a problem reading A/pix from FEI-style MRC files.
     *   New Processor for bit-compression of image files (makes images more compressible)

SPHIRE 1.3 major changes

* Support for processing helical specimens (beta).
* Hands free processing with AutoSPHIRE: While the individual steps can be configured and executed by hand, SPHIRE 1.3 includes AutoSPHIRE, an integrated tool that enables SPHIRE to run without the need for user supervision up until the creation of a high resolution reconstruction.
* Per particle CTF refinement with error estimation. When you reach a resolution of about 4Å you can refine your CTF on a per-particle basis. This can improve the resolution by 0.3Å or more.
* Integration of crYOLO 1.5 for particle picking. crYOLO is based on convolutional neural networks and can accurately pick about ten micrographs per second.
* Integration of automatic 2D class selection with Cinderella. This tool is based on a deep learning network to separate 2D classes from .hdf / .mrcs files into good and bad classes. It uses the same deep neural network as crYOLO and comes pre-trained on a set of good and bad classes. Cinderella was written to automate cryo-EM data processing.
* The new compare re-projections tool can now be used to produce side-by-side comparisons of the 2D class averages with the respective projections of a 3D model.
* Visualization of 2D power spectra in CTER.

--------------------------------------------------------------------------------------
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                      (www.bcm.edu/biochem<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_biochem&d=DwMGaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=msFqnaSgAGSIZpJQlaQ4dHlGx98f2jE8HwKZZJX9a9s&s=omPDeB4z0qd8OOA5S-en41lsZmuguqTcWJY_3EAoQc0&e=>)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__cryoem.bcm.edu&d=DwMGaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=msFqnaSgAGSIZpJQlaQ4dHlGx98f2jE8HwKZZJX9a9s&s=NtUFJBdpYaYOgtIGf5cH2vdFUlyEj7hMAXisFx_l0jM&e=>)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_research_cibr&d=DwMGaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=msFqnaSgAGSIZpJQlaQ4dHlGx98f2jE8HwKZZJX9a9s&s=VJVChMBgB4clQg4N6-Qq0vV0phgSus96DbTeqt_2Xcc&e=>)

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