Dear Consortium Members and Affiliates,
June news from the SBGrid Consortium includes a call for SBGrid user feedback on Dataverse, a link to watch our June webinar and details for joining our July presentation, some updates on SBGrid presentations to the community, a story on SBGrid member Leemor Joshua-Tor, a software release with 18 updates, three new members welcomes, and three member publication highlights.
The Dataverse Usability Team is recruiting SBGrid users for a short usability research study. SBGrid is collaborating with the open-source Dataverse Project to further develop SBGrid Data Bank hosting software. Volunteers are needed from July 18-July 21 to connect via GoToMeeting for ~45 min to try out some of Dataverse's new features while we observe ask for your opinions. Your participation will help improve Dataverse for researchers in Structural Biology and many other disciplines. Sign up to participate here.
If you missed our June webinar, featuring Trent Balius presenting on Dock, you can catch the recording on our YouTube channel. Mark your calendars for July 25th to hear the latest on BioXTAS RAW from Jesse Hopkins at Cornell University.
SBGrid staff have been active in recent meetings, with SBGrid PI Piotr Sliz talking about recent trends in structural biology computing and SBGrid support for electron microscopy at the Massachusetts Area Structural Biology Meeting at UMASS Worcester, and Pete Meyer, our SBGrid Data Bank lead, presenting at the ACA WK.04 on Research Data Management about recent improvements in the SBDB to support finding, citing, and reusing raw diffraction datasets. Thanks to the organizers for inviting us to present at these forums.
Cold Spring Harbor is the home base for Leemor Joshua-Tor, one of our newer members and the focus of our June member tale. Reflecting on her path to science, Joshua-Tor described how sense memory led her to chemistry and the squishiness of biology pushed her toward the precision of structural biology. For more on her background and the DNA replication and motor protein work happening in her lab, read the full story on Leemor Joshua-Tor.
For June we delivered a big software update, with updates to 18 applications including: AmberTools, autoPROC, BioXTAS RAW, BUSTER, CCP4, CTFFIND4, Dock, FOCUS, Geneious, HKL2MAP, pdb_extract, PHENIX, Rosetta, RELION, Schrodinger, SPHIRE, and XDS.
June brought us 3 new members: Steve Brohawn from UC Berkeley, John Pascal from the University of Montreal, and Olga Boudker from Weill Cornell Medical University. We also had two existing member transplants, with relocations for Georgios Skiniotis from U Michigan to Stanford and David Clapham from Boston Children's Hospital to the HHMI main campus where he now takes on the role of HHMI vice president and CSO. Welcome to our newest members and congratulations to those on the move!
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 Structural Biology Data Grid 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 received 4 new citations in the month of June. Thanks to all who remembered to acknowledge us: Raimund Dutzler from University of Zurich in eLife [Abstract]; Roderick MacKinnon from Rockefeller University in Cell [Abstract]; Holger Sondermann from Cornell University in Cell [Abstract]; and Pedro Pereira from the Universidade do Porto in Portugal in the Journal of Biological Chemistry [Abstract].
Over 50 publications from SBGrid member laboratories appeared in our latest monthly search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- From the laboratory of Erin Adams at the University of Chicago a new article in Immunity extends our understanding of the complex interactions between human leukocyte antigen F and NK cell receptors that may work to regulate immunity. [Abstract]
- HHMI investigator Tamir Gonen examines how the micro electron diffraction method is changing the science of cryoEM in a review appearing in Current Opinion in Structural Biology. He looks at the emergence of MicroED in 2013 and its future potential, and considers the basis selecting crystals and approaches to maximize success. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a paper from Georgios Skiniotis's group (recently relocated from U Michigan to Stanford) that appeared in Nature and opens up a new window into treatment options for Type 2 diabetes with high resolution structure of the insulin secretion hormone GLP-1 [More on Tumblr].
AmberTools version 17 is out with a fix to MDL SDF file reading and other minor improvements in the antechamber package as well as a fix to the way in which pytleap uses gaff2.
autoPROC is now at version 20170623. Two updates went out that include an option to create an XML file for multi-sweep datasets that are collected at a single wavelength, support for the latest XDS, default equal-number binning when merging statistics for STARANISO-processed data, removal of the trailing "/" from the -d/-I argument to avoid problems with links in summary.html, a new XML report for data after anisotropy analysis with STARANISO, and many other minor fixes.
BioXTAS RAW version 1.2.3. This version is a re-release that fixes a critical bug that could cause images to fail to integrate properly. This bug occurs only with numpy 1.12.
BUSTER version 20170620 includes improvements to Pipedream to allow input of compressed images and improve performance for raw images and summary.out statistics. A fix was also pushed for BUSTER pdbchk_element.
CCP4 is now at version 7.0.041.
CTFFIND4 version 4.1.8 is the new default. You'll notice that the Search was slowed for better accuracy, TIF files can be read on input, a new option to fix the amount and angle of astigmatism, data is resampled when the input pixel size is too small, a warning if CTF aliasing is detected, improved diagnostic 1D plots, and input movies need not be gain corrected (separate gain file can be given as input‚ or corrected for anisotropic magnification (via expert option)
Dock is now available in the SBGrid collection in two flavors - Dock 3 and Dock 6. Both are updated to the current versions 3.7 and 6.8, respectively. Dock 6 version 6.8 is the default version, but Dock 3 version 3.7-beta4 is also available via version override.
FOCUS is now at version 1.1.0.
Geneious version 10.2.2 introduces options to PCA plots for multi-sample RNA-seq data when comparing expression levels. There is also added support for cloning operations along with several other improvements and bug fixes.
HKL2MAP's latest update 0.4.e-beta supports "live" display of SHELXE auto-tracing models while the iterative auto-tracing/density modification process is running. It also connects several programs from the SHELX-suite to guide the user from analyzing scaled diffraction data (SHELXC), via substructure solution (SHELXD) and phasing (SHELXE), to displaying an electron density map (Coot).
pdb_extract version 3.22 was pushed out.
PHENIX version 1.12rc1-2801 updates Phaser to version 2.8
Rosetta 3.8 is now available and includes many new features. Version 3.8 includes a complete refactoring of XML supporting RosettaScripts, which offers many improvements, but will also require conversion of pre-3.8 XML scripts. You'll also notice the new JD3 allows crafting of more complex protocols, continuing improvements to how Rosetta handles unmodified PDBs, a new beta_nov15 scorefunction on the command line and in RosettaScripts, and refactoring of Rosetta's Ramachandran scoring code to support Ramachandran potentials for arbitrary amino acids.
RELION version 2.1beta implements the Stochastic Gradient Descent algorithm for initial 3D model generation. New functionality includes an option to impose helical symmetry in sub-tomogram averaging, and to impose local symmetry, much like non-crystallographic symmetry in X-ray crystallography.
Schrodinger 2017-2 includes usability improvements and performance enhancements across all of software.
SPHIRE is now at version 20170602 and includes an optimized ISAC algorithm for 2D Clustering to validate 2D class averages10-15x faster than before. Introduction of the polar coordinates methodology in MERIDIEN optimized parallelization, make it possible to determine a CryoEM structure within a few days on small clusters and desktop machines. RSORT3D was also improved, and new support was added for refinement of particles with icosahedral, tetrahedral, and octahedral symmetries.
XDS version 20170601 now accepts the new input parameter CLUSTER_NODES= for specification of processor nodes in a computer network and has automatic assignment of specified processors of a computer network for minimizing the wall-clock time for running XDS,
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.