Dear Consortium Members and Affiliates,
As we say goodbye to the last full month of winter here in New England, we look ahead with news on our May workshop, a profile on UC Berkeley's Jennifer Doudna, new webinars to watch, a date for our next SBGrid-Schrödinger Working Group, a software push with 14 updates and 2 new titles, and a few highlights from member publications.
We are currently accepting applications for Quo Vadis 2016: Advanced Crystallography. This 2-day course, focused on indexing, integration, and scaling of challenging datasets and initial model building in corresponding experimental maps, will be held May 23-24 at Harvard Medical School in Boston. Take a look at the preliminary program to apply. There are only a few spots left, so don't delay.
Jennifer Doudna, from University of California, Berkeley, is in the spotlight for our member webtale this month. Doudna gives credit to her high school chemistry teacher in Hawaii, who helped her see that much of science was about solving puzzles, for her approach to science: a "curiosity-driven" focus on the fundamentals rather than on finding cures.
For our March software webinar, we'll learn about the structure determination application CRANK2 (included in the CCP4 Suite) from Raj Pannu at Leiden University. Webinar details here. You can also watch our February webinar on BLEND, if you missed the live presentation, on the SBGridTV YouTube channel.
The SBGrid-Schrödinger Working Group will meet again in March, this time to hear more about Schrödinger's Protein Preparation Wizard. Join the discussion on March 29th and hear from Jas Bhachoo, Head of Education Initiatives for Applications Science from Schrödinger UK. More details here.
We're pushing out a large software update over the next couple of days. Watch for updates to BLAST+, CCP4, CrystFEL, DSSR, FASTA, GROMACS, HKL2MAP, ilastik, ImageJ, iMOD(NMA), MAFFT, PDB2PQR, SAMtools, and Spring, along with two new applications: Anaconda and MotionCorr. We're also cleaning up some old software versions to save space. But don't worry - we keep them handy and can quickly add them back upon request.
If you're no longer using 32-bit linux workstations, let us know! We can remove the 32-bit programs tree from your installation for faster updates and to free some disk space.
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.
For the month of January, SBGrid received 3 new citations in member publications, one from Tom Rapoport's laboratory at Harvard Medical School in PNAS. 2016 Feb 16 and two that appeared in Nature Scientific Reports from IBS Grenoble: Colombo et al. Scientific Reports. 2016;6:20876 and Lasalle et al. Scientific Reports. 2016;6:20629.
Over 50 publications from SBGrid member laboratories have appeared in journals since our last newsletter. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Phillipp Selenko's group at Leibniz Institute of Molecular Pharmacology in Germany published a pair of papers in Nature and Nature Communications that focus on the action of α-synuclein, a Parkinson’s disease-related protein. Using NMR and EPR they saw the protein's unstructured state in healthy cells Nature. 2016 Feb 4:45-50 and watched as a damaged version of α-synuclein introduced into healthy cells went about repairing itself. Nat Commun. 2016 Jan 25:10251.
- A new report from the NIH lab of Antonina Roll-Mecak looks at the effect of tubulin glutamylation on spastin, a microtuble severing enzyme. They found that glutamylation regulates spastin, but can also act as an inhibitor that can spread to neighboring microtubules. Cell. 2016 Feb 10.
- From our undergraduate desk, Harvard student Kristen Rodrigues highlighted two papers on Tumblr:
- One, a Nature story from Georgios Skiniotis's group at U Michigan published in collaboration with colleagues from several other institutes, that presents two holo-non-ribosomal peptide synthetase modules revealing their dynamic nature and providing insight into the structural basis of catalysis Nature. 529, 235–238 .
- Another appeared in the journal Structure from SBGrid members Eduardo Perozo and Robert Keenan and describes a new tool for the study of membrane proteins using nanodiscs.Structure. 2016. 24:300-9.
Software Changes
Anaconda version 2.4.1 is new to the SBGrid Suite. Anaconda is a Python distribution built for science, math, engineering, and data analysis. The package includes more than 400 of the most popular Python data analysis and visualization packages optimized for performance and parallel computing. Version 2.4.1 is built on python 2.7.11.
BLAST+ version 2.3.0 for Linux and OSX includes a beta release of SAM format, a new versioning policy, and support for single-file mode for BLAST XML2 and JSON formats so that results are delivered in a single file.
CCP4 version 7.0.003. This version includes the addition of balbes-pipeline and scaleit for CRANK2 along with a number of other bug fixes.
CrystFEL's latest version is 0.6.1 for Linux and OSX. This update includes a new prediction refinement step, an improved version of "partialator" for scaling and post-refinement, new indexing options using mosflm-cell and asdf, and new even-only and odd-only choices for process_hkl.
DSSR, now at version 1.4.7 for Linux and OSX has introduced a --nmr option for processing of NMR ensembles or trajectories of molecular dynamics simulations. Also new is a section summarizing structural features per nucleotide.
FASTA is now at version 36.3.8c for Linux and OSX. No additional information is available for this update.
GROMACS was updated to version 5.1.2 for Linux and OSX. This version includes fixes to mdrun and gmx tools, a new consistency check for double perturbation, and a number of performance improvements.
HKL2MAP version 0.4.c-beta is now the default for Linux and OSX. No additional information is available for this release.
ImageJ was upgraded to version 1.49 for Linux and OSX. The developers maintain a detailed list of all changes pushed out, so please be sure to check out their news page for details.
ilastik version 1.1.8 for Linux and OSX is the new default. With this version you'll see a new IIBoost Synapse Detection workflow, a new Object Statistics window, better support for multi-dimensional TIFF datasets, including OME-TIFF, along with many performance improvements.
iMOD(NMA) version 1.04 was pushed out for Linux.
MAFFT, now at version 7.271 was pushed out for Linux and OSX. You'll notice improved efficiency of parallelization when the number of sequences is large and sequence length is short, along with several bug fixes.
MotionCorr version 2.1 for Linux, is another new tool recently added to SBGrid. Motioncorr corrects whole frame image motion recorded with dose fractionated image stacks.
Spring version 0.84.1470 for Linux and OSX includes a new parameter to choose "out-of-plane tilt for amplitude correlation" along with several bug fixes and performance improvements.
PDB2PQR version 2.0 for Linux and OSX has an improved web interface. You'll also notice a new experimental interface - PDB2PKA - that can be used as an alternative to PROPKA for calculating pH values used to protonate residues. The developers stress the experimental nature of this new option.
SAMtools was updated to version 0.1.3 for Linux and OSX. A bevy of bug fixes and performance improvements are outlined in the full release notes, but the developers note a key change in the removal of the outdated sort subcommand. If you are still using sort ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead.
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.