Dear Consortium Members and Affiliates,
We have a brief newsletter for you before we sign off for the holidays, with a reminder that SBGrid will be closed between Christmas and New Years, a recommendation for users to try out our software installer, dates for January webinars, a profile of Tuft's scientist Katya Heldwein, a software release including 3 new titles and 5 updates, and 3 member publication highlights.
SBGrid staff and Harvard Medical School will enjoy a holiday break starting December 23rd. During the break we'll keep an eye out for emergencies, but the small stuff will stay on hold until the new year. We'll be back in full swing on January 4th. Happy Holidays to all!
Ready to try something new for the New Year? Give our new software installer a whirl. We've received lots of positive feedback about this handy new tool, which allows users to directly manage their SBGrid-supported applications from a simple graphical-user (Mac) or command-line (Mac or Linux) interface. Email us at accounts@sbgrid.org to register for the installer.
January brings back-to-back XFEL webinars, the first on January 10th will look at Processing serial crystallographic data using cctbx.xfel and DIALS with Aaron Brewster, and a second on January 17th will focus on Getting the most out of your XFEL data with IOTA and PRIME with Mona Uervirojnangkoorn and Art Lyubimov.
You can also watch our December webinar on YouTube and learn about xMDFF - a new molecular dynamics flexible fitting-based approach - with Abhishek Singharoy from the Beckman Institute and University of Illinois at Urbana Champaign. Watch now.
Katya Heldwein from Tuft's University is our featured member in December's member tale. With a primary focus on herpesviruses, Heldwein considers herself a structural virologist, examining these extraordinarily complex viruses from many different directions to understand their entry and exit from the cell. Read the full story.
Our December software release includes 3 new titles - GeRelion, PyOpenMM and QuSHAPE - and updates to 5 software applications: BioXTAS RAW, DIALS, EMAN2, and Scatter.
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.
SBGrid received 3 new citations in member publications during the last month, one in a Nature Communications article from Theodore Jardetzky's Stanford laboratory PDF and a two from Roderick MacKinnon's group at Rockefeller University in two different Nature publications appearing this month. Abstract1 Abstract2.
Over 52 publications from SBGrid member laboratories appeared in our December search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- In a new Science publication from Sebastian Klinge's group at Rockefeller University, researchers unveiled a 5.1 angstrom structure of the yeast small subunit processome, determined using cryo-EM, that provides a new framework for understanding previously reported biochemical data. Abstract.
- From one of our contributing developers, Alexandre Bonvin at Utrecht University, a new paper in the Journal of Molecular Biology describes enhancements to two software packages - DisVis. and PowerFit - and the new web-server interfaces that will allow more users to access these tools. PDF.
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a paper in Science to which SBGrid member Jay Nix, from the Molecular Biology Consortium at Advanced Light Source contributed, which describes the structure of Zika Virus xrRNA1 and a pseudo-knot that is essential for xrRNA1 function. More on Tumblr.
Software Changes
BioXTAS RAW version 1.2.1 is the new default. This version includes an improved EFA technique that can now be used with explicit, iterative, or hybrid methods for computing the concentration profiles of the components, and a new automated centering and calibration routine using the pyFAI library, for better determination of beam center and sample-detector distance.
DIALS was updated to the nightly release dev20161121.
EMAN2 release 20161215 is now in SBGrid.
GeRelion is new to SBGrid and version 1.1 was added. GeRelion is a GPU-enhanced version of RELION that dramatically speeds up 2D/3D classification and 3D auto-refine, from Maofu Liao's lab at Harvard Medical School.
PyOpenMM is another SBGrid addition. PyOpenMM, from Vijay Pande's group at Stanford, is a python API that wraps the OpenMM library (a tool for performing GPU-accelerated molecular modeling simulations).
QuSHAPE version 1.0.0 was added per a user request. QuShape is a comprehensive, platform-independent, user-friendly software package that enables efficient, reliable, and highly automated analysis of high-throughput capillary electrophoresis-detected nucleic acid chemical probing experiments. The developers strongly recommend using the SHAPE-MaP approach and ShapeFinder, which supersede QuShape and are also available in the SBGrid collection.
Scatter is now at version 3.0i. Since our last update the developers have modified the inverse Fourier transform to standardize the datasets before performing the transform, updated error estimates from the model using a Monte Carlo sampling method, and introduced several improvements to the Subtraction tab.
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.