Dear Consortium Members and Affiliates,
It's time for the penultimate edition of the SBGrid newsletter for this calendar year, with the the latest webinar news (Sjors Scheres and RELION up next!), 3 new sample preparation tutorials on YouTube, a software push with four updates and one new title, four new members to welcome, a reminder that CentOS8 is reaching end-of-life with suggestions for alternatives, and three member publications to highlight.
We had a flurry of webinars in November, with our regular webinar series running alongside a special series hosted in collaboration with Kurt Krause of University of Otago and Antoine van Oijen from University of Wollongong/ARC CCeMMP. When possible, we have added recordings of these talks to the SBGrid YouTube channel. Thank you to all of the speakers: James Bouwer, Yi-Wei Chang, Yifan Cheng, Lisa Eshun-Wilson, Tom Goddard, Tamir Gonen, Eric Hanssen, Yuntao Liu, William Nicolas, Shaun Rawson, Melanie Rug, Hari Venugopal, and Sara Weaver.
If you're struggling with sample preparation, we recommend 3 brief presentations in this YouTube playlist, with a panel of speakers covering preparation of vanishingly small to very large samples for single particle cryoEM, tomography and FIB milling, and MicroED.
This month's software push includes updates to AlphaFold, ChimeraX, IMOD, and Schrodinger, along with one new title: Voronota. See Software Changes below for complete details.
Four new members joined in November: Goran Bajic from Icahn School of Medicine at Mount Sinai, William Shih from Dana-Farber Cancer Institute, Michel Nussenzweig of Rockefeller University, and Stephen Burley of the RCSB Protein Data Bank. Welcome to our newest members!
Technical notes from our Software Team
CentOS 8 EOL 12/31
Red Hat is cutting short support for CentOS Linux 8, one of SBGrid’s two officially supported Linux distributions. This changes means that instead of reaching end-of-life in 2029, CentOS Linux 8 will no longer receive OS or security updates as of December 31, 2021.
CentOS existed as a community build of RedHat Enterprise Linux (RHEL) but is shifting to a testing build of RHEL known as “CentOS8 Stream.” Because stability was the primary reason for choosing CentOS over other Linux distributions, the prospect of moving to “Stream” has many users looking for alternatives.
New Support for Rocky Linux and Alma Linux
Two new Linux distributions aim to fill the hole CentOS will leave, building releases from RHEL: Rocky Linux and Alma Linux. Going forward, SBGrid will support CentOS 7, Rocky 8 and Alma 8. We also plan to support CentOS8 Stream, which is likely to see more updates than it had previously. We anticipate these will be relatively conservative since they are derived from RHEL updates, but that remains to be seen.
CCeMMP seminar series: To hear more about cryo-EM research and membrane proteins, sign up to the Centre for Cryo-Electron Microscopy of Membrane Proteins (CCeMMP) monthly seminar series. This seminar series will focus on research (cryo-EM of/or membrane proteins) and new advances in technology in the field with a mix of national and international speakers. Seminars are held 10:00-11:00am AEDT/AEST on the second Tuesday of each month. Register for Zoom details and calendar invitations for upcoming seminars. Seminars are recorded and made available on the CCeMMP website. Please register your interest - https://ccemmp.org/news/ccemmp-seminar-series/
Over 100 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:
Deposit your experimental datasets: If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.
Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.
Please use this SBGrid logo on the acknowledgements slide of your presentations.
We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software:
SBGrid citations: SBGrid's eLife paper received 3 new citations in the month of November, from these SBGrid-member laboratories: Alan Brown of Harvard Medical School in Cell: De novo identification of mammalian ciliary motility proteins using cryo-EM; Stephen Blacklow of Harvard Medical School in Structure: Crystal structure of the Tspan15 LEL domain reveals a conserved ADAM10 binding site; and Mark Lemmon, Joseph Schlessinger, and Daryl Klein of Yale University School of Medicine in Nature: Structural basis for ligand reception by anaplastic lymphoma kinase.
Alphafold 2.1.1 includes the new AlphaFold-Multimer model along with a number of other fixes.
ChimeraX version 1.3rc20211109, available via version override, includes improvements to the modeller comparative and modeller loops commands, which now support execution of a locally installed Modeller as an alternative to using the web service ("executableLocation" keyword), an option to directly edit model names and IDs in the model panel by double clicking on the name or ID and entering a new value, and a new define axis command to calculate best-fit axes (shown as cylinders) for use in distance and angle measurements and to specify vectors in other commands.
IMOD 4.11.11 is a bug fix release.
Schrodinger 2021-4 is out, with new features detailed here.
Voronota is new to SBGrid at version 1.22.3149. Voronota aids the analysis of atomic neighborhoods in molecular structures using a Voronoi diagram of balls determined from the atomic model, and is especially suitable for processing three-dimensional structures of biological macromolecules, such as proteins and RNA.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.
This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.
More information about the SBGrid Consortium is available at https://sbgrid.org
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