Dear Consortium Members and Affiliates,
It's time for the monthly SBGrid update that you have all been eagerly awaiting! This month we have a webinar you can watch (CrystFEL) and a webinar date to mark on your September calendar (HADDOCK), information on our 2nd Schrodinger Working Group presentation, a reminder to deposit your diffraction datasets in the SBGrid databank, a profile on NIH scientist Antonina Roll-Mecak, a welcome to one new member, eight software updates and one new application, and highlights from three member publications. Please read on for the details.
We had a good turnout for our CrystFEL webinar a couple of weeks ago. If you missed the presentation, you can watch the recording on our YouTube channel. We're taking a break for the month of August, but will resume on Sept 8th with a presentation from Alexandre Bonvin on HADDOCK. Details here.
Thanks to all who attended our first Schrodinger Working group. The first session was a high level overview, but our next webinars will be more focused, with a session on Molecular Dynamics with Desmond led by Dmitry Lupyan on September 15th and one on Docking in October. We've created a group mailing list for those that previously signed up to continue using Schrodinger. If you planned to sign up, but haven't yet had a chance, you can still register here.
We have a standing call for all members to deposit their diffraction datasets to the SBGrid DataBank. Follow this link to make your deposit: https://data.sbgrid.org/. If you're just beginning to prepare your paper for submission, check out our guidelines for how to deposit and cite the datasets in your publication.
For our July webtale, we spoke to Antonina Roll-Mecak at the National Institutes of Neurological Disorders and Stroke. Craking the tubulin code is the aim of Roll-Mecak and her group at the NIH, where they are using hybrid EM and X-ray crystallography approaches combined with single-molecule fluorescence to visualize microtubule activity. Read more of her story in the Member Tales section of our website.
David Corey, from the department of Neurobiology at Harvard Medical School, is our newest member. Welcome David!
Our July software release includes updates to CCP4, Geneious, Phenix, Python modules pandas and cython, R, Rosetta, and THESEUS. We also pushed out one new application: Spring. Read details in our Software Changes section below.
SBGrid member labs published over 75 manuscripts during the last month, a full listing of which can be found on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Jue Chen's group at Rockefeller University, published a story in Nature describing the structure of PCAT1, which acts as a pump to send proteins out of the cell and into the cell's environment. Read more in Nature. 2015 Jul 22;523(7561):425-30.
- From Alejandro Buschiazzo's group at Institute Pasteur Montevideo in Uruguay, we see the first high-resolution images of the Bovine Leukemia Virus's native capsid protein. Read the full story in the July 3rd issue of Science.
- Sean Crosson's laboratory at the University of Chicago gives us new insight into the Brucella abortus pathogen. Read more about this bacterium, which can jump from cattle to humans, and the conserved transcriptional regulatory system that Crosson describes in his PNAS publication.
CCP4 version 6.5.13 was pushed out this month. This is a minor bug fix release and corrects a problem with parallel processing in iMosflm 7.2.0.
Geneious was bumped to version 8.1.6. This upgrade represents a big jump with new features aplenty: 16S biodiversity tool, sequence classifier, new CRISPR design features, improved de novo assembly, new restrictions analysis options, and loads of other goodies.
Rosetta is now at version 2015.25.
Phenix nightly build version 1.10-pre2104 was pushed out, for those of you looking for the latest and greatest, if not the most stable, update. This version is not the default, but can be accessed using a version override.
Python module cython was upgraded to version 0.20.2 and 0.21.2, for Linux and Mac, respectively.
Python module pandas is now at version 0.15.2. This version includes enhancements to the handling of categorical data along with a number of other performance improvements and bug fixes.
Spring version 0.83.1449, was added to the collection. Spring (S ingle P article R econstruction from I mages of kN own G eometry) is a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.
THESEUS version 3.3.0 is an optimization and code cleaning release.
Please 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.