Dear Consortium Members and Affiliates,
January is blustering out with a howl as we send our first SBGrid update for 2019. Read on for details about our upcoming mini-symposium, a webinar for your calendar and one to watch now, a developer profile on Niko Grigorieff, a large software release with 18 updates and 1 new title, 3 new members to welcome, new position and event postings, and 3 member publication highlights.
SBGrid and NE-CAT will jointly host a mini-symposium in Boston, March 21-22. We're excited to have a great group of speakers focused on low-resolution model building in EM and X-ray crystallography. Thanks to all of the PIs who responded to our previous call for nominations. The workshop is fully subscribed and we look forward to hosting trainees from a diverse group of labs around the country in March. A preliminary agenda and links to additional event info are available on our website.
Many thanks to Thomas Grant from Hauptman-Woodward Institute for joining us last week for a webinar presentation on DENSS, a new tool for Electron Density Maps from Biological SAXS Data. Watch now on YouTube. Tune in later this month to hear from Tristan Bepler on Topaz: particle picking with positive-unlabeled learning. Full details here.
For our January developer tale we focus the spotlight on methods developer Niko Grigorieff, of HHMI’s Janelia Research Campus, who talks about his penchant for solitude, his plans to return to New England, and how he has turned rejection into its own kind of fame. Read the full story.
Our January software update includes new versions of autoPROC, BUSTER, CCP4, CCP-EM, Chimera, CTFFIND4, crYOLO, DIALS, DOCK6, Geneious, gnuplot, GPHL, HKL2000, NAMD, Phenix, Schrodinger, Shelx, and XDS. We also added one new title: PyEM
January brought us 3 new new members: Matthew Thompson from the University of Alabama, Elizabeth Wright at the University of Wisconsin-Madison, and Roman Melnyk of University of Toronto/Hospital for Sick Kids. Welcome to our newest members!
Events and Position Postings
The Harvard Cryo-EM Center for Structural Biology is looking for a cryo-EM specialist to join the team. The facility opened at the end of 2018 and currently houses two FEI Titan Krios electron microscopes, each equipped with a BioQuantum GIF/K3 direct detector, and one FEI Talos Arctica electron microscope equipped with a K2 direct detector. We seek personnel who will train users, operate the microscopes, and interface with a vibrant scientific user community. Full job description and information about how to apply here: https://cryoem.hms.harvard.edu
CCP4 and APS have announced their 12th annual School in Macromolecular Crystallography - June 17-24, 2019 - which will offer advanced training for researchers with some expertise in crystallography. The School includes lectures by software developers, data collection with samples provided by participants, and computing tutorials led by the lecturers. Lean more.
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.
I think we've reached a record, with 11 new citations for SBGrid's eLife paper appearing in member publications in the last month. We're grateful for the acknowledgements from:
- Sébastien Granier of Institut de Génomique Fonctionnelle in Nature Communications [Abstract]
- Harvard Medical School's Tom Rapoport in Nature [Abstract]
- Pedro José Barbosa Pereira at the Universidade Do Porto in Portugal in PNAS [Abstract]
- in a pair of publications from MIT's Catherine Drennan in Joule [Abstract] and ACS Chemical Biology [Abstract]
- another pair from Seth Darst at Rockefeller appearing in Nature [Abstract] and PNAS [Abstract]
- a new Nature article from Christopher Garcia's group at Stanford [Abstract]
- James Fraser, from University of California, San Francisco, in the American Chemical Society [Abstract]
- La Trobe University's Marc Kvansakul in his new FEBS Letters article [Abstract]
Over 30 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple notable highlights below:
- A new mini-review appearing in Biochemical Society Transactions from Christopher Hill of University of Utah describes recent advances in our understanding of the structure of the enzyme Vps4 and the molecular avenue by which it catalyzes the ESCRT pathways toward cellular membrane fission. Unraveling the mystery of the Vps4 mechanism may also help understand related AAA+ ATPases. [Abstract]
- In Nature Communications, Peter Kwong from the National Institute of Allergies and Infectious Diseases has a new paper, co-authored with DFCI's Joseph Sodroski, in which they present studies on the potency of small-molecule inhibitors of HIV-1 entry, notably BMS-818251, and introduced a crystal lattice for structure determination of the HIV-1 Env trimer-entry inhibitors complex. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight the latest publication from Navtej Toor's University of California, San Diego laboratory that appeared in Nature Communications. The publication describes solving the crystal structure of the group IIB intron immediately prior to the second stage of splicing and presents a model for this second step of RNA splicing. [More on Tumblr]
autoPROC was updated to the 20181127 snapshot. New features include support for latest versions of XDS (20180808), CCP4 (7.0.066), POINTLESS (1.11.17) and AIMLESS (0.7.3) and for HDF5 datasets, for extracting axis definitions from Eiger/HDF5 images (e.g. "/entry/sample/transformations/omega"), for the XDS plugin mechanism, and for extracting experiment descriptions (detector axes and incident beam direction) from HDF5 metadata file. For the Diamond (DLS) beamline, there is new support for I24 images written in fullCBF format.
BUSTER snapshop 20181127 includes updates to Pipedream with new pepflip and SideAide binaries, the addition of modelcompare, a new PDB_REDO component, and an improvement in Pipedream to write cell dimensions of reference model and experimental data to summary.out. This update also includes a BUSTER build system upgrade to Intel Compiler version 16 and the optimisation library from PETSc 2.3.2 (with TAO 1.8.2) to PETSc 3.10.2; a new -td command-line option to "grade_PDB_ligand" that defines a temporary directory in which all the intermediate files are saved, and new support for individual atomic anisotropic displacement parameter (ADP) refinement.
CCP4 version 7.0.067 was updated with a new DIALS workaround for old matplotlib, a fix to cctbx to add the missing cma_es, an updated binary for shelxe, and bug fixes to zanuda.
CCP-EM is now at version 1.2.0, which now includes a pre-compiled copy of RELION v2.1, LocScale improvements so MPI mode works on both Mac OS X and Linux, and a new option in Refmac for automatic detection of symmetry in atomic models.
Chimera version 1.13.1 squashes several bugs, including a fixes to the Align Chain Sequences tool, to a problem with using rotamers of proline from the Dunbrack 2010 rotamer library, and a bug that mis-identified element types in new Amber trajectories. New support was also added for independent rotation in Animation scenes.
CTFFIND4 version 4.1.13 changes include the addition of the radial "equi-phase" average of experimental spectrum in bottom right quadrant of the diagnostic image, improved search options, new expert options to set OpenMP (-j command-line option overrides interactive user input), and changes to the score, which is now a normalized cross-correlation coefficient.
crYOLO version 1.2.2 was pushed out.
Dock 6 version 6.9 adds de novo DOCK (DOCK_DN), an enhanced chemical searching method that is a de novo design method and can be used to construct molecules from scratch or modify existing molecular frameworks, and adds a new fragment library generator function to the docking protocol that is accessible through flexible ligand docking.
DIALS version 1.12.3 fixes EIGER detector support, allows combining output_file with imageset_index in dials.export_bitmaps, and add xia2 fixes to encoding in the HTML log and to restore the previously removed xia2.to_shelx command.
Geneious, now known as Geneious Prime 2019.0.4 is the new default.
GNUPLOT version 5.2 has new options for plot styles, improvements to the polar mode, the addition of nonlinear coordinate systems, along with a number of new command and terminal options.
GPHL - Global Phasing Suite, for commercial users, is now at version 20181127.
HKL2000 version 718 is now available.
NAMD version 2.13 includes improved GPU performance with support for non-orthogonal periodic cells, new kernels for bonded force terms, and CUDA support for advanced features. This version also incorporates several new and improved methodologies, with the stochastic velocity rescaling thermostat, REST2 for improving sampling efficiency, hybrid QM/MM simulation new interleaved double-wide sampling for alchemical FEP, a new constant-pH MD implementation, Gaussian accelerated MD (GaMD) to reduce energetic noise in the post-processing, and the enhanced sampling protocol τ-Random acceleration MD (τRAMD).
Phenix dev-3374 is now available via version override.
PyEM 0.3 is new to SBGrid. PyEM is a set of Python modules and command-line utilities for electron microscopy of biological samples.
Schrodinger update 2018-4 is now available.
SHELX was updated to version 2019-1.
XDS version 20180808 is now available. You'll notice improved error handling during the INTEGRATE step caused by the absence of strong spots for determination of reflection profile parameters. Also new is a change in XSCALE, which now accepts the input parameter REIDX_ISET= to allow users to reindex reflection indices specifically for each input data set.
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.