Dear Consortium Members and Affiliates,
With the holidays upon us, we have an early and abbreviated monthly newsletter to share that includes holiday closure details, a profile on SBGrid member Deb Kelly, a webinar wrap-up and look ahead, a software push with ten updates and one new title, and two member publication highlights.
SBGrid is closed from December 20th to January 2nd for the holidays. We'll have a skeleton crew watching out for emergencies, but will otherwise plan to pick things up again in the new year. Happy holidays to all!
Deb Kelly is the focus of our December SBGrid Tale. We spoke to her from her lab at Penn State where she uses cryoEM in her cancer research on BRCA1 and P53, and in more recent studies into SARS-CoV-2 proteins. But Kelly is also taking the cryo out of electron microscopy, using the lens of liquid and air to get a fuller picture of the virus in action. [Read the full story]
Our webinar series closed for the year with presentations from Sjors Scheres on RELION-4.0 and Yuntao Liu on IsoNet. Both presentations are now posted to the SBGrid YouTube channel. Webinars will restart mid-January and really get rolling in February. Mark your calendars, or better yet, subscribe to SBGrid's public calendar at https://sbgrid.org/calendar/.
This month's software push includes updates to CCP4, ChimeraX, DIALS, EMAN2, Geneious, NMRFAM-Sparky, Phenix, PyMOL, Scipion, and Xplor-NIH, along with one new title: Julia. See Software Changes below for complete details.
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:
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 December, from these SBGrid-member laboratories: Hao Wu from Boston Children's Hospital in Cell: NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation; Alan Brown from Harvard Medical School in Nucleic Acids Research: Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates; Sichen Shao from Harvard Medical School in Nature Structural and Molecular Biology: Structural insights into metazoan pretargeting GET complexes.
CCP4 release 7.1.018 is now available.
ChimeraX 1.3 is now available as a stable release.
DIALS was bumped to release 3.7.1.
EMAN2 nightly build 20211129 is out and available via version override.
Geneious 2022.0.1 is out and includes new options to automatically annotate your ORFs, CDS and mRNA regions using BLAST, to easily add and remove optimized codons to your sequence, to use a command line interface to run Geneious as part of your broader bioinformatic pipelines locally, to highlight mismatching base calls in your chromatograms, and even includes a beta dark mode to try out.
Julia is new to SBGrid. Julia is a flexible and dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
NMRFAM-Sparky build 4/22/21 is now available.
Phenix 1.20 includes several new tools for using the predicted models from AlphaFold, including the Phenix AlphaFold2 notebook to run AlphaFold on Google Colab from Phenix GUI, along with functions to identify useful domains in AlphaFold model, dock domains of AlphaFold model into cryo-EM, rebuild the AlphaFold model in a cryo-EM map using docked domains, and process, dock and rebuild AlphaFold model with cryo-EM map. See the change log linked above for full details.
Scipion was updated to 3.0.9.
Xplor-NIH was bumped to version 3.4 and includes improved facilities for using electron density projections in structure calculations, ability to handle .mrc(s) electron density files larger than 2GB, improvements to the genLigand.py script in eginput/PSF_generation to deduce bonding in the absence of CONECT records, to create .top and .par files from an input PDB file, along with many bug fixes, documentation improvements, and optimizations.
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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