Dear Consortium Members and Affiliates,
Just like that, the year is gone, and we're getting our newsletter out to you early this month, before holiday travels begin. Read on for details about SBGrid's holiday break, January webinar plans, a profile on SBGrid member Michael Rosen, a big software push with 18 updates, 3 new members to welcome, and a couple of member publication highlights.
Tuesday, December 24th is the beginning of the SBGrid holiday break, when SBGrid and all of Harvard Medical School will close up shop for the holidays. We'll be out from December 24-January 1, and while we'll keep an eye out for emergencies, the small stuff will stay on hold until after the break. See you in 2020 and Happy Holidays to all!
In webinar news, we'll hear about what's new in VMD from the Theoretical and Computational Biophysics Group at U of Illinois Urbana-Champaign on January 28th. John Stone and Abhishek Singaroy will present. Cinderella was on the roster for December, but we ran into a conflict and Thorsten Wagner is now rescheduled to give you a Cinderella primer in March. [Webinar details here].
We took a trip to the south for our December SBGrid Tale, to hear from Dr. Michael Rosen at University of Texas Southwestern Medical Center in Dallas, where his lab was an early entrant in the hot field of phase separation and finds himself, like many others, making the leap from NMR into microscopy. [Read the full story].
We have a big software push going out before the end of the year. Look for new versions of Chimera, CCP-EM, crYOLO, DIALS, FOCUS, Geneious Prime, HKL2000, ilastik, ImageJ, NMRFAM-Sparky, OpenMM, MAFFT, MoRDa, ORCA, Topaz, Schrodinger, Situs, and Xplor-NIH. See Software Changes below for complete details.
December brought us 3 new members, with Aaron Gregory Schmidt joining a growing contingent at Massachusetts General Hospital along with new users from Vertex and Ribometrix. Welcome to our newest members!
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:
• Josh Chappie of Cornell University investigates the McrBC restriction system and bacterial defense in a new paper in the Journal of Biological Chemistry. The authors present findings from their solved structures of the Thermococcus gammatolerans McrB DNA binding domain (Tg∆185) both alone and bound to a methylated DNA substrate, uncovering a new means of substrate recognition and specificity among McrB homologs.[Abstract]
• In Nature Immunology, Sun Hur of Boston Children's Hospital reviews the current literature on the innate immune signaling pathways triggered by the detection of cytosolic nucleic acids with a focus on the regulatory mechanisms, notably the cGAS–STING for DNA and the RLR–MAVS for RNA. A greater understanding of the mechanisms that check the activity of cytosolic nucleic acid sensors could offer new therapeutic targets for human diseases. [Abstract]
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:
Structural biology applications used in this project were compiled and configured by SBGrid .
 A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
Link to article: https://elifesciences.org/articles/01456.
SBGrid's eLife paper received 4 new citations in the month of December, from these SBGrid-members: Sanofi researchers Ronnie Wei and Dana Lord (now at Ohana Biosciences) in this Nature Cancer publication Trispecific antibodies enhance the therapeutic efficacy of tumor-directed T cells through T cell receptor co-stimulation; Lawrence Stern of University of Massachusetts Medical School in Nature Communications: In vivo clonal expansion and phenotypes of hypocretin-specific CD4+ T cells in narcolepsy patients and controls; Harvard Medical School's Alan Brown, in the bioRxiv article: Structure and activation mechanism of the BBSome membrane-protein trafficking complex; and from Holger Sondermann's laboratory at Cornell University in mBio: A Conserved Regulatory Circuit Controls Large Adhesins in Vibrio cholerae.
Chimera 1.14 is now available. This version updates AmberTools to version 18, includes new Previous/Next buttons to speed moving through and between model display and/or activation, removes Area/Volume from Web from Surface/Binding Analysis because the NIH StrucTools server is no longer available, adds an option to get annotations from the Conserved Domain Database (CDD) from Multalign Viewer (Sequence), adds improvements to MD Movie to preserve the PSF segment name as a residue attribute segment, and reports the segment names to the Reply Log as the trajectory is read, and fixes a number of bugs.
CCP-EM version 1.4.1 fixes a bug in the CCP-EM install script when CCP4 version >= 7.0.078 is installed.
crYOLO 1.5.4 is the new default. This version includes a fix to systematic offset when picking K3 images using the general model, introduces a fix to stop a crash when minimum distance filter is used, adds a “Print cmd” button to the GUI, and fixes a bug that caused crYOLO to stop working when no filtering is used.
DIALS is now at version 2.0.2. With the bump to 2.0, users will notice many changes, including symmetry determination and scaling, used by default in xia2, flexible workflows for challenging data, speed improvements across the code base to address more challenging data sets, more consistent output file naming, dials.cosym and xia2.multiplex for multi-crystal analysis, Python 3 compatible code (this is currently experimental, but will be fully supported in the next major release).
FOCUS was updated with the latest nightly build, available via version override.
Geneious Prime was updated to version 2020.0.3. This update includes several new features. Clustal Omega replaces the ClustalW aligner, giving greater scalability and improved alignment quality. Back translation and codon optimization were also improved, along with annotation of CDS features from a reference Database
HKL2000 is now at version 720. This release adds support for the Eiger2 format (detectors 16M, 9M, 4M, 1M) and for the h5 nexus format for Diamond beamlines. In addition, users can now display scaling statistics for different .sca files to visually compare results, edit starting and ending frame numbers for .x data sets, and use "HKL Builder" to refine the structure with the twinning mode enabled.
ilastik was updated to 1.3.3, which now includes support for n5 volumes, for masks in Pixel Classification, Atlas Mask overlays for Object classification, arbitrary data types for autocontext, along with lots of internal fixes.
ImageJ 1.52 is now available. See the ImageJ website for detailed release notes.
NMRFAM-Sparky was updated to version 20191119
OpenMM 7.4 is focused on performance improvements for functions related to simulations. You'll notice increased speed when creating a System from a ForceField, building water boxes and membranes, loading PDB files, and sometimes when creating a new Context. This release also includes classes for simulated tempering and metadynamics and support for PPC processors such as Summit. The developers have also prepared the code that will work with the functional forms used in the HIPPO force field (Jay Ponder's group is currently developing as the successor to AMOEBA).
MAFFT version 7.453 is the new default.
MoRDa version 30 is now available.
ORCA 4.2.1 is now available to those labs who have registered for the software. You can find detailed release notes on their website.
Topaz version 0.2.3 was pushed out and includes improvements to the pretrained denoising models, new pretrained particle picking models, updated tutorials, an updated GUI to include denoising commands. You can also find the developers' new Denoising paper preprint here.
Schrodinger 2019-4 release notes are available here.
Situs put out a patch release to version 3.1 rev2.
Xplor-NIH version 2.52 is the new default. New in this version is HBPot, a hydrogen bonding geometry potential of mean force. You'll also notice fixes to terms for refinement against chemical shifts, a new headerHelp facility which provides info on items in the headers in the output PDB files, and many bug fixes, performance optimizations, and improvements to documentation.