Dear Consortium Members and Affiliates,
The holiday season is upon us and we took advantage of some quieter days around Thanksgiving to push a bunch of software updates. Read on for news about our latest webinars, a look at Daniel Panne in our member tale, new position postings from member labs, a software push with 12 updates and 3 new applications, two new members to welcome, and three member publication highlights.
We've got back-to-back NMRPipe webinars coming up on December 5th and 12th. Frank Delaglio will present on "Concepts in Spectral Processing of Conventional and Non-Uniformly Sampled NMR Data" and "Processing of Conventional and Non-Uniformly Sampled NMR Data with NMRPipe." Full details on our website. Don't forget that you can also catch Steven Ludtke's October presentation on EMAN2.2 on our YouTube channel.
For our October member tale, we connected with Daniel Panne, of the European Molecular Biology Laboratory in Grenoble. Panne describes his focus on chromatin and the linguistic connection he sees in the language of gene regulation. Read the full story.
Be sure to look at some of the newly listed open positions from SBGrid member labs: Electron Microscopy IT Coordinator at Harvard Medical School; postdoctoral and research assistant positions in the Deaconescu Lab at Brown University; and a research associate position in Dr. Julien’s laboratory at The Hospital for Sick Children Research Institute. If you'd like us include a position posting for your group, please email Michelle. [Job Postings Page].
We have a big list of software changes for you this month, with updates to 3DNA, BioXTAS RAW, CUDA, DSSR, EMAN2, GROMACS, HKL2000, Jalview, NMRPIPE, RELION, Scatter, and XDS. We also added three new titles: Plumed, crossflaghkl, and NMRFx-Processor.
Two new members joined in November: Eva Nogales from UC Berkeley and Lauren Jackson from Vanderbilt University. Welcome to our newest members!
Member Publications
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.
Five new citations popped up for our SBGrid eLife paper during November. Thank you to Alexandre Bonvin at Utrecht University [Abstract], University of Utah's Chris Hill [Abstract], Jean-Philippe Julien at University of Toronto [Abstract], Tom Rapoport from Harvard Medical School [Abstract], and our friends at the Protein Data Bank Europe [Abstract].
Our Member Publications listing is back up and running and includes over 50 articles emanating from member labs. You can find complete details on our website, along with a couple of notable highlights below:
- Katherine Henzler-Wildman of the University of Wisconsin-Madison has a new publication in PNAS that provides a helpful, new model for EmrE transport in E. coli that seems to resolve the conflicts arising from the pure exchange model. The new free-exchange model explains EmrE’s ability to bind diverse substrates, helps broaden our understanding of proton-coupled transport. and opens up novel ways for manipulating this small drug resistance transporter for drug discovery. [Abstract]
- Continuing the theme of new models, Chris Fromme from Cornell University has a new paper in the Journal of Cell Biology that elucidates the function of the transport protein particle complex TRAPPIII in wild type yeast. Studying the role of TRAPPII in activating the molecular switch GTPase Ypt1 (the mammalian homologue of which is Rab1), Fromme's team provides a compelling model for TRAPPIII function in eukaryotic cells. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a new article in Nature Communications published in collaboration with Dartmouth's Jason McLellan which describes a potential therapy for respiratory synctial virus usin a small molecule inhibitor targeting RSV fusion. More on Tumblr.
Software Changes
3DNA is now at version 2.3.1-20170624. You'll find a new --cif (or --mmcif) option to the 3DNA rebuild/fiber programs to output generated structures in the standard PDBx/mmCIF format, which is especially useful for large structures which are out of the limit of the classic PDB format.
BioXTAS RAW version 1.3.1 fixes several small bugs and includes new citation information for the new RAW paper.
crossflaghkl is new to SBGrid, from software developer Tim Grüne. crossflaghkl partitions a merged hkl-file into k subsets with the number of reflections marked with -1.
CUDA was updated to version 9.0.126
DSSR, at version 1.7.2-20171120, has had several small updates since our last push: an added module to automatically identify and fully characterize G-quadruplexes, refined algorithms for identifying H-bonds and base pairs for boundary cases, changed type=O to type=X for eXtended A-minor motifs to avoid confusion with the previously documented type 0, and lowered the default angle for splayed-apart dinucleotides from 100 degrees to 85.
EMAN2 version 20171116 is now available.
GROMACS version 2016.4 includes fixes to mdrun and gmx tools, improvements to documentation, and portability improvements including support for CUDA 9/Volta for nonbonded kernels.
HKL2000 version 716 is out and includes several new features: a "site included" option that allows one to place the def.site file in the data (frames) or processing directories - instead of in a directory in the hklint sites directory; 6 additional scaled (.sca) files are generated, using scalepack with auto corrections, which are tuned for tasks like displaying radiation damage and anomalous maps, structure refinement, and generating statistics; Xdisp Qt is now the default frame display program; "Check Space Group" is integrated with the "pointless" program from CCP4, allowing users to apply the selected space group for the next scaling and auto generates required re-indexing matrix; a new 'Merge' tab allows users to combine 2 or more .sca files.
Jalview version 2.10.2b2 was pushed out. You'll notice major changes since our last update, including a new Ensembl REST client to retrieve annotated genes, transcripts and proteins; new options in the Calculations menu's 'Show cross-references' to show Ensembl as well as EMBLCDS and Uniprot when CDS/Protein mapping data is available for download or display; more accurate structure mappings; option to import structures from PDBe as mmCIF, new search dialogs for UniProt and PDBe Free Text Search, and an improvement to the alignment column ruler, with numbering according to the reference sequence.
NMRPipe is now at version 20171120.
NMRFx Processor 10.1.15 is another new title. NMRFx Processor is software for processing multi-dimensional NMR spectra featuring quality and performance to handle complex data analyses. Note that due to licensor restrictions, we can only add this software to an installation for nonprofit users who register with NMRFX & submit confirmation to SBGrid.
PLUMED 2.3.3 is the last of our new titles for this month. PLUMED is an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines to p erform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.
RELION version 2.1b1 was updated with the latest version of CUDA 9 to fix some memory allocation problems.
Scatter is now at version 3.1r.
XDS version 20171111 now accepts the RGRID= input parameter so the user can define the grid size of the histogram for finding difference vector clusters in the IDXREF step, which overrides the defaults. The output file header generated by XSCALE now contains the cell constants of each included input data set to help detect non-isomorphism and identify compatible subsets of input data
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.