Snow, snow, beautiful snow. With over 100 inches falling on Boston this winter, there's nothing left to do but embrace it. Between blizzards we've had a few other things going on, including plans for a RELION webinar, a story on Navtej Toor from UCSD, a new shared resource for Cryo-EM data processing, a software analytics initiative, a software release that includes 9 updates, two new members, and highlights from a few of excellent papers recently published from SBGrid member labs. Be sure to follow us on twitter.com/sbgrid to keep up on all the daily news happening at SBGrid.
For our March webinar we'll hear about RELION from Sjors Scheres of the MRC on March 24th. Connection details are posted on sbgrid.org. A number of you already joined us for Harry Powell's iMosflm presentation last Thursday. We'll be uploading this webinar to our YouTube channel soon, so be sure to subscribe to receive updates when new videos are added.
Our February Tale puts the spotlight on Navtej Toor from the University of California, San Diego. Dr. Toor describes his fascination with introns and their evolution -- a topic he believes deserves more attention -- and the path he followed to solve his recent structure.
SBGrid members can now access a new shared resource, with our recent deployment of a server for processing Cryo-EM data. This machine has 64 cores, 512 Gb of shared memory, and is stocked with the SBGrid programs collection. It is intended for short-term EM projects (1-2 months), but longer term access for larger projects can be provided on a cost-sharing basis. For more information please visit our forum article or email us at firstname.lastname@example.org to request access.
We are also launching a pilot Software Analytics initiative to help developers assess the usage and impact of their software and allow SBGrid to more efficiently update and maintain the collection. SBGrid and its members depend on the generosity of the software developers who contribute their programs for our use. To support their efforts we'll be collecting statistics on an application's use and total hours used, operating systems, and crash occurrences. No user- or group-identifiable information will be stored. This project is supported through NSF EAGER award #1448069. If you have questions or would like to opt-out of our data collection process, please contact our Policy Fellow, Andrew Morin, at email@example.com. You can read more about the SBGrid Software Analytics initiative in /programs/share/ANALYTICS.
Nine software updates were pushed out during the last month. You'll find new versions of ARP/wARP, CCP4, GAMMA, HKL2000, Phenix, PyMOL, Rosetta, Schrodinger, and xplor-NIH in your software tree. Read more about these changes in our Software Changes section details below.
The month of February brought us two new SBGrid members, both representing institutions new to SBGrid: Jason McLellan from the Giesel School of Medicine at Dartmouth College and Jason Schnell from the University of Oxford in the UK. Welcome to our new members!
We're also highlighting a few of our members' high profile papers that recently appeared in journals. Read our Publications section below for more about these papers and a link to a listing of over 38 other publications emanating from SBGrid member labs. If you have a new technology that was recently deployed in your lab, please let us know by emailing Michelle Ottaviano or communicating with SBGrid on Twitter (@SBGrid). We will share your news with SBGrid community.
How is SBGrid cited? Here are some recent member publications that cite SBGrid's eLife publication:
- Peersen Lab in J. Virology: “Model building, refinement, and validation were performed with Coot, Phenix, and MolProbity, respectively, as distributed via the SBgrid consortium (31).”
- Drennan Lab in JACS: “The structure was completed with SBGrid compiled software (26).”
- Toor Lab in Nature: Structure refinement was done using Buster, Phenix, DEN and Phenix. .... All software was compiled by SBGrid (43).
- Garcia Lab in Nature: "All Software was compiled by SBGrid (198)."
ARP/wARP was updated to version 7.5. This update includes improvements to protein model, beta-strand, DNA/RNA, and solvent building, enhancements to Fit Ligand, which now includes the 84 most common ligands, and upgrades to the auto-depth view and ArpNavigator menus. Note: Users must register for ARP/wARP before it will appear in the default download. Registration details here.
CCP4 is now at version 6.5.0 003. This version fixed setup scripts for MANPATH, incorporated some improvements to 6-fold screw analysis (more work is needed), and wiped out several bugs.
GAMMA version 4.3.2-413 is a bug fix release from Gamma's subversion repository.
We pushed out the latest for HKL2000 - version 706c. This version recognizes the Bruker detctor Photon 100 and now allows users to load a site file from the site configuration window.
Phenix now incorporates nightly build dev-1951, our first phenix nightly build from phenix's new buildbot builds and installer.
PyMOL was updated to the latest version, 220.127.116.11, which includes fixes for the stereo background bug, Tcl/Tk menu logging settings, and picking when cartoon_debug is set.
Rosetta was updated to version 2015.05, the most recent weekly release of Rosetta.
With Schrodinger version 2014-4 the Maestro GUI has been improved, size limits were Increased for ligand docking, and KNIME was updated to the latest version.
We now have the latest version of XPLOR-NIH. With version 2.38 users will see a bevy of bug fixes and optimizations in addition to improvements in handling ensemble weight optimization, plotting in the calcTensor helper, and trajectory writing/reading from the Python interface.
SBGrid member labs published over 38 manuscripts during the last 30 days, a full listing of which can be found on the Member Publications page of the SBGrid website. Here are some notable highlights:
On the EM front, Axel Brunger's group from Stanford University determined an ~8Å structure of the NSF/SNAP/SNARE (20S) supercomplex, which is responsible for disassembly of individual SNARE components and making them available for subsequent rounds of membrane fusion. This work was published in a Nature article on February 5th. Another impressive EM structure came from Nenad Ban's group at ETH Zurich. In their NSMB paper they describe a budding yeast initiation complex and reveal an efficient lysine cross-linking protocol that loosely tethers proteins to allow formation of a stable assembly. Pam Borkman's group from Caltech developed a different cross-linking technology. In the Jan 29th edition of Cell they demonstrated that DNA cross-links can increase the potency of antibodies against HIV. Meanwhile Benjamin Schuler’s group, from ETH Zurich, published their use of single-molecule spectroscopy to study the assembly dynamics of the cytolytic pore toxin ClyA in the Feb 5th edition of Nature Communications .
With more and more SBGrid groups utilizing Schrodinger in-silico docking software (available to all North American groups) for HT docking computations on our shared clusters at HMS, we are starting to see some encouraging success stories. On February 1st Biogen IDEC, an SBGrid group located in Cambridge, MA, published a manuscript describing structure-based design of low-nanomolar PIM kinase inhibitors. On the X-Ray crystallography front Jennifer Doudna's group determined a structure of the Dicer-TRBP complex.
Please contact us if you have a new technology that was recently deployed in your lab. You can also communicate with SBGrid on Twitter (@SBGrid).
Don't forget to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
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.