Dear Consortium Members and Affiliates,
We hope this Halloween edition of the SBGrid newsletter will lift your spirits, with new webinars on EMAN2 and the Phenix-Amber integration, an alert for anyone looking to update to Mac OS Catalina, 20 software updates, one new member to welcome, a deadline to register for the NECAT Symposium, and 3 member publication highlights.
Many thanks to Nigel Moriarty for joining us for our October webinar. If you missed his presentation on integrating the Amber force field into Phenix, watch now on the SBGrid YouTube channel. NEXT UP: join us November 12th to hear from Steven Ludtke on In-situ and in-vitro subtomogram averaging to subnanometer resolution using EMAN2.3. Webinar details here.
Operating System Alerts: for those of you looking to buy new computers or update existing Mac or Linux machines, please note:
- SBGrid IS NOT COMPATIBLE WITH MacOS 10.15 "CATALINA", the latest version of Apple's MacOS that was recently released. With Catalina, Apple is enforcing strict filesystem controls that will break SBGrid installations. They have also dropped support for 32-bit binaries that many older applications require. We strongly recommend that you DO NOT upgrade to 10.15 on any Mac with SBGrid software. A solution is in the works, but it may take some time before we can fully implement the changes to officially support 10.15. We are also compiling a list of 32-bit software applications that we can no longer support after machines are updated to version 10.15.
- CentOS 8 SUPPORT COMING SOON: CentOS 8 was released on 9/24 and we are testing SBGrid with plans to add support for this Linux distribution in the near future. We are not there yet, so hold off on those updates for now, but we expect the transition to be relatively smooth. With the addition of support for CentOS 8, we will move our build pipeline to CentOS 7 and begin phasing out support for new titles on CentOS 6.
We had a big software push this month, with updates to 20 titles: ARP/wARP, BUSTER, CCP4mg, crYOLO, DIALS, EMAN2, FASTA, Geneious, IMOD, iMosflm, pdb_extract, Phenix, RELION, RELION 3.1-beta, RStudio, Schrödinger, Slingshot, SPHIRE, TensorFlow, and Topaz. See Software Changes below for complete details.
One new member joined the SBGrid ranks this month. Welcome to Sarah Bowman of Hauptman-Woodward Medical Research Institute.
Community Announcements / Position Postings
NOV 1 REGISTRATION DEADLINE: NECAT is hosting a symposium, Crystallography in the 21st Century: Reflections on Raj Rajashankar. Register here to celebrate Raj's life and his contribution to science, and hear from a terrific lineup of speakers on November 8th at the Italian Academy in NYC from 8:30am - 5pm. Cost is free, but registration is required.
Over 70 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:
- In response to the increase in drug resistance, doctors are searching for new options for inhibiting Bruton’s tyrosine kinase (BTK), which is targeted in the treatment of immune cancers. Amy Andreotti of Iowa State University has a new paper in PNAS that unveils a new target, the PH/kinase interface, which offers a new avenue for therapeutic discoveries. [Abstract]
- In Acta Crystallographica Samuel Butcher of the University of Wisconsin-Madison works to expand the currently limited repertoire of solved RNA structures by reporting the structure of an RNA helix with pyrimidine mismatches and cross-strand stacking. The authors focused their study on CUG repeats, thought to be responsible for the heritable, multi-system disease, myotonic dystrophy type 1 (DM1). Their study reveals the high structural diversity of the pyrimidine-rich regions of RNA and contributes to our understanding of RNA conformational space. [Abstract]
- From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication from the laboratory of John Kuriyan that appeared in Nature Immunology in which the authors investigate the kinetics of T cell activation with a focus on activation of the LAT scaffold and the function of tyrosine residue Y132. [Read more]
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.
October brought some new citations for our eLife publication, with references appearing in 6 new journal articles from Samuel Butcher's group at the University of Wisconsin-Madison in Acta Crystallographica: Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking; Daved Fremont of Washington University, St. Louis, appearing in BioRxiv: Structural basis of cowpox evasion of NKG2D immunosurveillance; The Hospital for Sick Children's Jean-Philippe Julien in BioRxiv: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs; Adam Frost and Wesley Sundquist's laboratories at University of Utah in BioRxiv: Membrane constriction and thinning by sequential ESCRT-III polymerization; Frank Sicheri's University of Toronto group in the Journal of Molecular Biology: Structural and Functional Analysis of Ubiquitin-based inhibitors that Target the Backsides of E2 Enzymes; and IBS Grenoble in Cell Host and Microbe: Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01.
ARP/wARP is now at version 8.1.
BUSTER 20191003 is the new default. This version adds explicit hydrogen-hydrogen contacts for hydrogens at electron-cloud or nuclear position, adds missing torsion angle restraints to the Engh&Huber amino-acid restraint dictionary involving hydrogen atoms, improves the aB_hydrogenate script to give detailed information about dictionary provenance for actual hydrogenation step, adds better weights for a (new) B-factor restraints database, and introduces many other bug fixes and performance improvements.
CCP4mg is now at version 2.10.10, which includes a number of significant improvements with support for https downloads from EBI, new icons for all "applications", restoration of PDB search functionality, an option to select/color by PDB "entity", a new inside color options for maps, a new default to color the aromatic ring by first carbon atom color, if present, an update to ffmpeg version to 3.3.3, improvements to MrBUMP, new automatic "Coot-style" fog and clipping options and atom-clicking, and updates to Python 2.7.14.
crYOLO version 1.5 includes a new GUI (start with cryolo_gui.py), an optimized fast low-pass filtering pipeline, a new monitor mode for prediction, a new rotation data augmentation option, an option to change the number of layers for fine tuning (-lft), and a new command - cryolo_evaluation.py - to output an html file with the results.
DIALS was bumped from 1.14.3 to 1.14.12. See the change log for a full list of updates for each iteration.
EMAN2 version 2.31 is the new default. New features in EMAN2.3 include a complete CryoET pipeline from tilt series through subnanometer resolution hybrid subtomogram averaging, fiducial-less fully automated tilt series alignment (also works with fiducials), rapid tiled Fourier reconstruction, full tilt/geometry aware CTF correction, a multi class 3-D particle picker with new ties to deep-learning annotation, SGD automatic initial model generation, traditional 3-D subtomogram averaging, per-particle per-tilt hybrid subtomogram/single particle reconstruction to subnanometer resolution, a new switchable filter in e2boxer making it dramatically easier to distinguish particles in images, improvements to bispectral classification for 2-D unsupervised classification and 3-D refinement, focused classification in 3-D refinement available from the workflow interface, improvements to e2extractsubparticles as an alternative to focused classification, and an upgrade from Qt4 to Qt5 as part of the process of transitioning to Python3 over the next year.
FASTA version 14-aug-2019 is the new default.
Geneious patch release 2019.2.3 is now available.
IMOD was updated to version 4.10.34 for Mac.
iMosflm version 7.3.0 allows users to read hdf5 files directly, adds options to process HDF5 files from the latest Dectris Eiger2 and Quadro detectors, and ".img" files from Rigaku Pilatus and Eiger detectors, introduced a feature to sum images when doing spot-finding for indexing (Eiger and Pilatus detectors only), calculates error estimates for refined detector parameters and prints them to the mosflm.lp file. Users will also notice new warning messages when i) optimization of the measurement box parameters has not worked optimally; ii) the profile tolerance parameters have been increased to help deal with images where the spots are not well resolved, or iii) too many reflections are flagged as too wide in phi, along with many other bug fixes and performance improvements.
pdb_extract 3.24 includes improvements to the calculation of the entity_poly groups, a fix to _refine_ls_shell.R_factor_all, and improves handling of special residue names, such as "Cr","Ar", "Gr", "Ur".
Phenix version 1.17 improves handling of SHELX data in Phenix.
RELION 3.0.8 is the latest stable release. Users will notice an update to relion_mask_create that fixes --and, --or, --and_not, --or_not, improvements to Refine3D, a fix in Extract to repair uninitialized variables that resulted in wrong OriginX/Y values of the first particles in each micrograph, and a GUI vix to allow the use of --reconstruct_subtracted_bodies in continuation. With public beta testing of RELION 3.1 ongoing, the developers will only address critical bugs in 3.0.x going forward.
RELION 3.1-beta is available via version override for the adventurous. This beta version includes high-order aberration correction in CTF refinement (see https://www.biorxiv.org/content/10.1101/798066v1), an external jobtype to run third-party software in the relion pipeline, schedules for designing & executing on-the-fly processing procedures, and tweaks to the GUI, pipeliner and helical processing.
RStudio 1.2.5001 introduces a new Slurm plugin for the Job Launcher that enables running R sessions and jobs on Slurm clusters, adds support for starting and managing Jupyter sessions alongside R sessions, and overhauls the user dashboard for managing R and Jupyter sessions, and jobs.
Schrödinger version 2019-3 is the new default.
Slingshot was updated to version 1.3.2
SPHIRE 1.3 includes support for processing helical specimens (beta), a new option for hands-free processing with AutoSPHIRE, new per-particle CTF refinement with error estimation, integration of crYOLO 1.5 (for particle picking) and Cinderlla (for automatic 2D class selection), a new compare re-projections tool to produce side-by-side comparisons of the 2D class averages with the respective projections of a 3D model, visualization of 2D power spectra in CTER, and other minor bug fixes.
TensorFlow 2.0 was pushed out. With this version the developers have put a focus on ease of use, including the addition of Keras as the central high level API used to build and train models, including eager execution, for immediate iteration, intuitive debugging, and tf.data, for building scalable input pipelines.
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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