Dear Consortium Members and Affiliates,
For our June update we have a status update on our new MacOSX installation client, a webinar recording along with our lineup of speakers for the summer and fall, a story on Nick Sauter and DIALS, a new SBGrid software environment, access to the SBGrid git repository, a software push with 15 updates and 2 new applications, 9 new members to welcome, 2 SBGrid citations, and 3 member publication highlights.
The first beta test for our GUI-based MacOSX installation client is now underway. Thank you, beta testers, for helping squash bugs in these early builds. If you did not sign up for our first round of beta testing, you can sign up for round two by completing this google form.
On the webinar front, last week Ivet Bahar gave us a tutorial on the protein structural dynamics application ProDy. If you missed the live presentation, you can watch the recorded version on SBGrid's YouTube channel. Looking ahead we just finalized our webinar lineup through December, so please mark your calendars for these presentations:
July 26 - Christian Olsen on Geneious
Sept 13 - Daniel Cappel on PyMOL
Oct 4 - Willy Wriggers on SITUS
Nov 1 - Willy Wriggers on Sculptor
Dec 6 - Abhishek Roy on xMDFF (a VMD plugin)
For our June webtale we talked with Nick Sauter and learned a little about his path into structural biology, from the myoglobin structure he first learned about in his tenth grade honors biology course to his role leading the development of DIALS at Lawrence Berkeley National Labs.
After months of testing we are rolling out a new SBGrid software environment. As the SBGrid software collection has grown, the size of the SBGrid shell environment has grown with it, leading to slower performance at the terminal, longer shell initialization times, and even slower application performance. With this update we aim to provide a new environment that is completely compatible with the legacy shell while offering new features and better tools for us to support software. We think you'll notice significant performance gains across applications, more responsive GUIs, and near-instant shell initialization. And there are no modules to load or new commands to learn! We will be deploying this new environment to your site in the coming days (the legacy environment will still be available) and welcome feedback.
Did you know SBGrid consortium members have access to our SBGrid git repository? Use distributed version control to keep your projects moving with free private repos. Share code within labs and with collaborators. Request an account at accounts@sbgrid.org and check it out at https://git.sbgrid.org.
Our monthly software release includes updates to CrystFEL, DIALS, EMAN2, Gamma, Geneious, Gnuplot, NAMD, NMRPipe, PyMOL, Scatter, SIMPLE, Simulaid, Tigris, XDS, XDSGUI, and two new applications: XDSCC12 from Kay Diederichs's group and Sculptor from Willy Wriggers.
We've had 9 new members join since our last report: Robert Lefkowitz from Duke University, Andrés Palencia from University Grenoble-Alpes, and a large contingent from EMBL Heidelberg including Janosch Hennig, Orsolya Barabas, Carsten Sachse, John Briggs, Martin Beck, and Christoph Müller. Welcome to our new 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.
For the month of June, SBGrid received 2 new citations in member publications: one from Ron Rock's group at the University of Chicago in Biophysical Journal Biophys J. 7:2517-27 another in JACS from Catherine Drennan's laboratory at MIT J Am Chem Soc. 2016 Jun 21.
Over 70 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:
- A study from Peng Gong's group at the Wuhan Institute of Virology in China looks at 7 crystal structures from enterovirus 71 revealing mechanistic details in initial NTP binding, active site closure, and postcatalysis movement of the RNA duplex when vacating the active site. Read more in PNAS. PNAS. 2016 Jun 23.
- For those of you just beginning to dip your toes in the waters of Python programming, Cameron Mura's group at the University of Virginia has published a basic introduction to Python coding to help you better manipulate your data. To get started, check out this primer in PLOS Computational Biology. PLoS Comput Biol. 2016.12:e1004867.
- From our undergraduate desk: Harvard student Kristen Rodrigues highlighted a new publication from Theodore Jardetzky’s group at Stanford University that appeared in Nature that gives insight into how omalizumab therapy works for asthma patients and suggests that omalizumab in combination with a mutant IgE-Fc fragment might block basophil activation more efficiently Read more on Tumblr.
Software Changes
CrystFEL's newest version, 0.6.2, includes improved stability for the scaling algorithm and new custom dataset splitting" in partialator, a new default to "retry" indexing will delete the weakest few peaks and try again to index a pattern, and a new option to prepare a map giving the saturation value for each pixel individually.
DIALS was updated to version 20160520.
EMAN2 nightly release 20160621 is now available.
Gamma was updated to version 4.3.3.
Geneious was patched with version 9.1.5, which includes bug fixes and other minor changes.
Gnuplot is now at version 5.0.3. Since the last update you'll find new plot styles "with parallelaxes" and labeled contours, a new "set xdata geographic" coordinate system (Degrees, Minutes, Seconds), updates to the "fit", which can now handle functions with up to 12 variables, an option to lock secondary axes (x2, y2) to the primary axis via a mapping function, and many other minor updates.
NAMD is at version 2.11 and includes many new features: performance enhancements for GPU-accelerated simulations, enhancements to Tcl scripting, improvements to the collective variables module, including to histogram bias, and replica-exchange multiplexing.
NMRPipe version 20152224 is the new default.
PyMOL version 1.8.2.1 fixes the mutagenesis wizard “No Mutation” (update and rms commands), adds a new “pick32bit” setting to force 16bit picking, and fixes the pse_binary_dump + pse_export_version<1.77 combination
Scatter was rebuilt and optimized in version 3c. This version also includes many new features, such as automated trace calculation for HPLC SEC SAXS, SVD-based averaging, a multiple dataset similarity comparison tool, and a new method for Guinier Peak Analysis.
Sculptor is new to SBGrid from Willy Wriggers's group. Sculptor is a GUI-based extension of the Situs docking programs to allow interactive multi-resolution docking and visualization for low-resolution density maps and atomic structures.
SIMPLE version 2.1 has major revisions to the PRIME (PRobabilistic Initial Model generation for single-particle cryo-Electron microscopy) code with a new PRIME SAC solver included in simple_prime2D and improvements to the ab initio 3D reconstruction code in simple_prime3D, which is now ~ 150 times faster.
Simulaid is now at version 20160611.
Tigris version 0.31 is the new default.
XDS version 20160517 accepts new input parameters: EXCLUDE_DATA_RANGE to exclude data images from processing and FIT_B-FACTOR_TO_REFERENCE_DATA_SET to force the isotropic temperature factor of the processed data to match the corresponding one of a reference. You'll also notice a new option in XDSCONV to save structure factor amplitudes and intensities in MTZ files.
XDSCC12 is new to SBGrid from Kay Diederichs group at the University of Konstanz. XDSCC12 generates delta-CC1/2 values.
XDSGUI version 20160520 includes many bug fixes, a delta-CC1/2 plot, and a renaming of the XDSSTAT tab to Statistics.