Newsletter

Dear Consortium Members and Affiliates,

Begone, scram, skedaddle. We're shooing 2020 out the door with an early update from the SBGrid team, and the final one for 2020. We have news about our holiday break, links to our latest webinars along with our 2021 lineup (with a focus on EM software tools), a reminder about our library of past EM webinars, a small software update, one new member to welcome, 2 member publication highlights, and warm and healthy wishes to all for a safe and happy new year! 

SBGrid and all of Harvard Medical School will take a holiday break beginning December 21 and continuing through the New Year. The day-to-day stuff will sit on the back burner through the holidays, but we'll watch out for emergencies. See you in the New Year!

We closed out the year with 3 science talks - webinars from Prof. Vera Moiseenkova-Bell at University of Pennsylvania, Matt Jaremko of Leemor Joshua-Tor's group at Cold Spring Harbor Laboratory, and Lejla Zubcevic of the University of Kansas Medical Center. Many thanks to all 3 for terrific presentations and for fielding questions from attendees. Check our YouTube channel for some of the recordings:  https://www.youtube.com/user/SBGridTV.

With almost 150 videos available, SBGrid's YouTube channel is a great resource for new structural biologists just getting familiar with the software and more experienced researchers taking a deeper dive to learn new techniques. Our electron microscopy playlist includes 22 videos and we're kicking things off in 2021 with tutorials on emClarity, DeepEMhancer, GPU ISAC, Coot, and CryoAssess. Not every webinar is recorded, so be sure to join us online for the live presentation, where you'll get  a chance to ask developers questions directly.

Our software push includes updates to autoPROC, Buster, CCP4, Chimera, COOT, crYOLO, GPHL, ISOLDE, PHENIX, PyMOL, Scipion, and TranSPHIRE. See Software Changes below for complete details.

December brought us one new member from the University of Michigan: Shyamal Mosalaganti. Welcome to our newest member!

Technical notes from our Software Team

Changes at the CentOS project
For many years we have recommended CentOS, the community-built Linux distribution that tracks Red Hat Enterprise Linux (RHEL) releases. RedHat recently announced CentOS 8 will become CentOS Stream, a development branch of RHEL no longer based on the stable RHEL release. This change makes CentOS considerably less suitable for production workloads, and the stable release of CentOS 8 will now reach end-of-life at the end of 2021.

We recommend that users stick with CentOS 7, which is supported until 2024. We're watching to see what the future holds for CentOS and for other new community builds of RHEL that may be in the works. We'll update our recommendations as the situation develops.

Apple Silicon Macs
Apple released the first of its new ARM64 "apple silicon" macs this month. We are testing the SBGrid software stack on the M1 chip and, so far, compatibility and performance look very good. Most of the SBGrid applications work on the new M1 CPU with macOS 11
and Apple's Rosetta compatibility environment. Standards like COOT, PyMOL, Chimera, CCP4, and PHENIX work seamlessly, but there are exceptions (CCPEM, RELION). We expect to support most titles on BigSur with the new M1 hardware early in 2021.

Installation path changes coming in 2021
In early 2021, we're moving the default installation path for the SBGrid software collection to /opt/sbgrid.  This path is already the default for our CLI and Mac installation manager, and rolling it out to all installations will eliminate the need for a /programs symlink, provide, better compatibility with new macOS filesystem restrictions, and make administration for HPC environments easier. No action is needed at this time. Look for announcements in 2021.

Member Publications

Over 50 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:

If you're currently preparing a manuscript, please remember you can publish your datasets in the SBGrid Data Bank along with your PDB record deposit and publication submission to preserve your primary experimental datasets. We also recommend the following boilerplate language in all publications that report results obtained with SBGrid supported software:

SBGrid's eLife paper received 2 new citations in the month of December, from the laboratories of SBGrid members:  Thomas Schwartz at MIT in Nature Communications: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif;  Demetrios Braddock, Elias J. Lolis, and James Murphy of Yale University School of Medicine in PLOS ONE: Unraveling the mechanism of recognition of the 3’ splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60.

Software Changes

autoPROC version 20201210 is now available.

BUSTER version 20201210 is the new default.

CCP4 is now at version 7.1.009.

Chimera 1.15rc includes updates to APIs to address the retirement of legacy RCSB PDB web service APIs, which impacted the fetching of UniProt sequence annotations and mmCIF entries. Support was also added for Gromacs 2020 trajectories.

COOT was updated to version 0.9.3.

crYOLO version 1.7.6 fixes a library issue.

GPHL 20201211 is now available for industry members with a license.

ISOLDE 1.1.0 works with all the new ChimeraX features and includes a few other improvements: an update to adaptive torsion restraints to a more flexible form, all N- and O-linked glycans now automatically gain extra restraints on first simulation, and performance improvements eliminate long delays when adding new ligands or waters.

Phenix is at version 1.19-4080. With the bump to 1.19

phenix.real_space_refine has improved rotamer fitting and map/restraints weight calculation, and morphing can now use multiprocessing. Two new methods were added -  phenix.local_resolution, to calculate a local resolution map, and phenix.local_aniso_sharpen, to optimize a map taking into account local resolution-dependence and anisotropy of the map and its errors. There are also new high-level scriptable Python tools for map and model analyses and manipulation.

PyMOL  was bumped to version 2.4.1

Scipion 3.0.6 is the new default

TranSPHIRE 1.5.13 sets project pattern as default for the Project Name and fixes a performance issue when using e2proc2d.py.

 

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.

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More information about the SBGrid Consortium is available at https://sbgrid.org

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