[3dem] Release of the latest version of SPHIRE

[Stefan Raunser]

Dear EM community,
We are excited to announce the release of the latest version of our SPHIRE  software suite (SPHIRE Beta Patch 1) (co-distributed with EMAN 2.2 and SPARX) , which is now available from our website:

http://sphire.mpg.de<https://urldefense.proofpoint.com/v2/url?u=http-3A__sphire.mpg.de&d=DwMGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=33GhWmUzxWDoNEEn95TH3nVcJvAy4a6HebLeBCyb3z4&s=04Ujzq5G-7aHzNO3rcVP6wb1Ky6TLXcYMuYf4-aaFC0&e=>

Main new components and updates:

- ISAC2 – Rapid and stable 2D Clustering
We optimized the popular ISAC algorithm for 2D Clustering (Yang et al., Structure, 2012). ISAC yields now validated 2D class averages > 10-15x faster than before.
In addition, the new Beautifier tool allows further refinement and sharpening of the ISAC 2D class averages in order to reveal high-resolution features in 2D.

- MERIDIEN – Rapid ML 3D Refinement
We introduced the polar coordinates methodology (Penczek et al., 1992) and optimized the parallelization of the program to speed up the structure refinement, reduce the memory requirements and enable calculation on single nodes.
MERIDIEN is now > 10-15x faster than the previous version.
Cryo-EM structure determination with SPHIRE is now possible within a few days on small clusters and desktop machines.

- RSORT3D – Reproducible 3D sorting
We re-implemented and improved the 3D sorting procedure and methodology. The updated RSORT3D is 3-4x faster and capable to run on desktop machines.  More importantly, it produced better results for several high resolution projects in our lab.

- Icosahedral, Tetrahedral and Octahedral Symmetry
Refinement of particles with icosahedral, tetrahedral, and octahedral symmetries is now supported.

- Easy installation
The release of SPHIRE Beta Patch 1 is synchronized with the release of EMAN 2.2. The new Anaconda Installer allows a fast and smooth co-installation of both programs. At the moment we only support CentOS, but we work hard on developing a MacOS Installer for the upcoming stable release.

For any issues and inquiries, the SPHIRE team is accessible almost 24/7 via the mailing list.<https://urldefense.proofpoint.com/v2/url?u=https-3A__listserv.gwdg.de_mailman_listinfo_sphire&d=DwMGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=33GhWmUzxWDoNEEn95TH3nVcJvAy4a6HebLeBCyb3z4&s=yUJ84BmoBfUZa5j2o-lur1OlwjeDwOroamLEgH_Ic-o&e=>
We sincerely hope that the updated SPHIRE Beta Patch 1 version will meet your expectations and be a helpful advance in high-resolution cryo-EM.

Your SPHIRE development team

Toshio, Markus, Felipe, Thorsten, Michael, Christos, and Stefan – MPI Dortmund

Zhong and Pawel - UTH Texas

(Follow us on Twitter: https://twitter.com/SPHIRE_Package)

---------------------
Stefan Raunser, Ph.D.

Director, Department of Structural Biochemistry
Max Planck Institute of Molecular Physiology
Otto-Hahn-Str. 11
44227 Dortmund, Germany
tel: +49-231-133-2300

and

Adjunct Professor, Faculty of Chemistry and Chemical Biology
Technical University Dortmund

Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology
University Duisburg-Essen

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