Dear Consortium Members and Affiliates,
Along with the heaps of snow that March brought to us in Boston, we got back on track with our webinar series, wth a new presentation on cryo-EM in the Cloud. Read on for what's next and a story on Harvard Medical School member, Andrew Kruse, a big software update, a request for feedback from the SPIDER developers, a welcome to one new member, and 3 publication highlights.
Many thanks to Michael Cianfrocco for his webinar presentation last week on cryo-EM in the Cloud. For those of you who missed it, stay tuned; we'll be adding the recording to our YouTube channel soon. Next up we'll hear from Woonghee Lee at the University of Wisconsin-Madison about NMRFAM-Sparky. Join us April 3rd at 12pm EDT.
Harvard Medical School's Andrew Kruse is the subject of our March Member Tale. Kruse gave us some background on his turn from llamas to yeast in his effort to cut the cost and time associated with membrane structure studies, and how the new yeast platform he helped to develop, recently described in Nature, and a new computational structure approach, are opening new avenues of understanding. [Read the full story]
We pushed out a big software release this month, including updates to CAVER, Caver Analyst, CCP4, ChimeraX, Coot, DIALS, EMAN2, Gctf, Geneious, Gromacs, MAFFT, MISO, MotionCor2, NMRPIPE, ORCA, PEET, Phenix, PyMOL, RELION, Schrödinger, SCIPION, SHELX, XDS, and XPLOR-NIH.
An update to SPIDER is in the queue for next month, and we're passing along a call for feedback from the developer, asking users: Do you see a continued use for SPIDER in your laboratories?. We know anecdotally that when our SPIDER distribution breaks, our community raises the red flag immediately. Please let us know your thoughts, or contact the developer directly.
We had one new member join in March. Welcome to Feng Zhang at MIT.
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the SBGrid Data Bank along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
SBGrid's eLife paper got 4 new citations in March, appearing in publications from Youxing Jiang at UT Southwestern Nature [Abstract], Jason McLellan, now at UT at Austin, in PLOS Pathogens [Abstract], Seth Darst from Rockefeller in eLife [Abstract], and Pedro José Barbosa Pereira from University of Porto in Journal of Biological Chemistry [Abstract]. Thanks for remembering us!
More than 65 member publications appeared in March journals. You can find a complete listing on our website, along with a few notable highlights below:
- In Nature Scientific Reports, Enrico Di Cera of St. Louis University studies the move from the E* to E conformation of the zymogen prothrombin during activation to the protease thrombin following ligand recognition. As key components of the blood coagulation system, a better understanding of the molecular steps of activation can elucidate the cause of and suggest treatment for blood clotting disorders, as well as develop a reference for zymogen activation in blood coagulation and fibrinolysis. [Abstract].
- Harvard Medical School's Suzanne Walker has a new publication in the Journal of the American Chemical Society that uncovers, via a protein microassay method developed in the lab, the role of the asparagine ladder in substrate recognition by the enzyme O-GlcNAc Transferase. OGT is a key player in the regulation of numerous cellular processes and has been implicated in cancer, diabetes, and neurologic disorders. This discovery could lead to the ability to predict OGT substrates and thus, manipulate O-GlcNAcylation for scientific and therapeutic ends. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues highlighted a new publication co-authored by Tim Springer of Boston Children's Hospital that appeared in Science. Using polarization-based microscopy, the authors evaluated ligand-bound integrin alignment to understand how integrins receive cues from their environment about directional force. [More on Tumblr].
CAVER 3.02 is the new default. Since our last update you'll find corrections to the starting point optimization procedure, a new default of 4 letters in residue name while reading the PDB files, with an option to return to the three letter mode, an option to user letters in the atom serial number, useful when loading large PDB files, and a more efficient version of the UPGMA clustering algorithm.
Caver Analyst 2.0 beta was pushed out.
CCP4 got bumped a couple of versions to 7.0.051. This version includes updates to Arcimboldo, Ample, CCP4i, DIALS, Phaser, and Simbad. CCP4i also includes numerous bug fixes, a new crystal definition and interface.
ChimeraX was updated to version 0.5. This release includes ViewDockX, for analyzing molecular docking results, and the ability to show nucleotides as ladder rungs or slabs.
Coot is now at version 0.8.9.1. This update includes a new function to limit the display radius for models, a change so the refinement map is set before refinement of solutions in ligand fitting, improved Ramachandran Plot, now with residue selection, use of threads and accumulation in map contouring, a secondary structure interface added to the API, a new toolbar button - user-defined modelling - to refine tandem residues, a new experimental peptide orientation optimisation function added, and many other performance improvements and bug fixes.
DIALS is now at 1.9.0 and includes support for scan-varying beam models, a renaming of dials.discover_better_experimental_model to dials.search_beam_position (#418), a fix to avoid crashes in Ubuntu 14.04 (#513), and an improvement to dials.image_viewer so it will work with large Nexus files.
EMAN2 version 2.21a fixes a bug causing a "missing SNR" problem during refinement, better support for bispectrum-based class-averaging and 3-D refinement and GPU in Neural Network tomogram segmentation and particle picking, adds support (early version) for phase plates in CTF correction with adjustable phase slider and autofitting, improves the GUI display of CTF and Astigmatism, and fixes bugs in e2symsearch3d and subtomogram averaging.
Gctf version 1.18 was pushed out, a special version for phase plate that is available via version override.
Geneious 11.1.2 is the new default. Since the bump to 11, key new features incluce an option to annotate potential restriction sites that can be introduced by silent mutations, new Volcano Plots to visualize gene expression in an interactive view that synchronizes your selection with the Annotations and Sequence View, improved Fastq Import to to allow paired reads to be associated with each other to set read technology during import. You'll also notice CRISPR Improvements, with added support for Cpf1 enzyme variant with 5' PAM site and now 'Target Sequence' as a qualifier on CRISPR annotations.
Gromacs has a new release: version 2018. They have rolled out performance improvements (with and without GPUs) to allow users to run PME long-ranged interactions on a single GPU, which means many fewer CPU cores are needed for good performance, and there is new optimized SIMD support for recent CPU architectures: AMD Zen, Intel Skylake-X and Skylake Xeon-SP. Other new features include new support for the AWH method, an adaptive biasing method used for overcoming free energy barriers and calculating free energies, a new dual-list dynamic-pruning algorithm for short-ranged interactions that uses an inner and outer list to permit a longer-lived outer list, while doing less work overall and making runs less sensitive to the choice of the “nslist” parameter, and a new physical validation suite, which runs a series of short simulations to verify the expected statistical properties.
MAFFT is now at version 7.394.
MISO version 0.5.4 is now available.
MotionCor2 pushed out a bug fix release and is now at version 1.0.5.
NMRPIPE is now at version 20180301.
ORCA bug fixes were pushed out with version 126.96.36.199.
PEET version 1.12.0 updates MATLAB to R2017b and uses a 64-bit mex interface, adds flgParallel and helices to programs seedSpikes and spikeInit, automatically saves vertical alignment motive lists, reads subvolumes faster, adds the parameter flgSearchAlongParticleAxes, and adds two new programs: createRotAxesFiles and scoreHistogram.
Phenix nightly build dev-3063 is now available.
PyMOL version 2.1 has new selection keywords "polymer.protein" and "polymer.nucleic" and supports SpaceNavigator and "auto_copy_images" on all platforms.
RELION version 2.1 has a new implementation of the Stochastic Gradient Descent algorithm for initial 3D model generation, adds functionality to impose helical symmetry in sub-tomogram averaging and to impose local symmetry, much like non-crystallographic symmetry in X-ray crystallography.
SBGrid Infrastructure updates pushed out during the last quarter include a variety of performance improvements to the Installation Client, along with improvements to the Installation Client registration page, and a new Webinars page on the website, to easily view the full collection of SBGrid-hosted webinars.
Schrödinger 2018-1 is the new default.
SCIPION version 1.2.beta is now available as a version override.
SHELX version 2018-2 includes updates to SHELXE, SHELXL, and SHELXT. See the changelog for full details.
XDS was updated to version 20180307. Since our last update, this version has revived the refinement routine used in Version June 1, 2017 (BUILT=20170615), which is more suitable to correct errors in the specification of the detector distance, and often improves data quality. There is also an improved algorithm in the IDXREF step, for recognizing a lattice basis of unknown crystals, and slight changes in the meaning of parameters controlling vector clusters in the IDXREF step; RGRID=, SEPMIN=, CLUSTER_RADIUS=.
XPLOR-NIH version 2.47 includes fixes for eefxPot, prePot, and planeDistPot so they work better with strict symmetry, the addition of CLYS patch for generating di-ubquitin, improvements to targetRMSD handling of files with differing PSFs, a reworking of eginput/psl examples to improve reproducibility and ease of use, and many other bug fixes and improvements.
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.