Dear Consortium Members and Affiliates,
We're writing with our last bit of news for 2017, before we sign off for the holidays, with a reminder that our office will be closed starting Friday, with links to watch two new webinars from Frank Delaglio, the latest position postings in member labs, a summary of recent software updates, 11 (!) new members to welcome, and 3 member publication highlights.
Starting December 22nd SBGrid and Harvard Medical School will close for a holiday break. During the break we'll watch out for emergencies, but the small stuff will stay on hold until after new year. We'll be back in full swing on January 2nd. Happy Holidays to all!
We've posted two new webinars from Frank Delaglio, of NMRPipe fame, on our SBGrid YouTube channel. Part One focuses on Concepts in Spectral Processing, while Part Two digs deeper into Processing of Conventional and Non-Uniformly Sampled NMR Data with NMRPipe. We've had a couple of speaker cancellations for our 2018 lineup, so we're currently inviting a new round of speakers and will post online soon with more details.
You can read about the latest open positions in SBGrid members labs on our Position Postings Page. If you'd like us to include a new opportunity available in your lab, please email Michelle.
We have a big list of software changes for you this month, with updates to ADXV, ACEMD, ATSAS, BCFtools, CCP4, ChimeraX, DIALS, Geneious, PEET, PHENIX, PyMOL, SAMtools, and XDS, and one new application: cisTEM. We've also summarized the changes pushed out to the SBGrid Install Client and website this past quarter. Full details in the software changes below.
December brought us 11 new members. Carlos Escalante became our second at Virginia Commonwealth University and a big group of labs joined from UCSF: Adam Frost, David Agard, Yifan Cheng, Charles Craik, Seemay Chou, Aashish Manglik, Daniel Minor, Oren Rosenberg, Daniel Southworth, and Robert Stroud. Welcome to our newest 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 SBGrid Data Bank 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's eLife paper got 4 new citations in December, with mentions from Catherine Drennan at MIT in Science [Abstract], Holger Sondermann at Cornell in the J. Biological Chemistry [Abstract], Borden Lacy at Vanderbilt in the J. Biological Chemistry [Abstract], and SBGrid members on each coast - Stephen Blacklow and Andrew Kruse at Harvard Medical School, SBGrid's own Pete Meyer, Georgios Skiniotis at Stanford, and Dimitar Nikolov at Memorial Sloan Kettering - who contributed to this Cell publication [Abstract].
Over 75 member publications appeared in journals in December. You can find a complete listing on our website, along with a couple of notable highlights below:
- Available online in PNAS this month is a new paper from Karin M. Reinisch & Thomas Walz, of Yale University School of Medicine & The Rockefeller University respectively, elucidating the structure of the PI4KIIIα complex. Following the axiom that communication is key to the success of relationships (in this case, cellular relationships), the benefit of studying this lipid kinase complex lies in its role in the phosphorylation of plasma membrane phosphatidylinositol to produce the multifunctional phosphoinositides, which are responsible for cell signaling as well as the regulation of almost all aspects of membrane activities. [Abstract]
- In a new publication in Science, Catherine Drennan's group at MIT has solved the structures of methylphosphonate synthase & hydroxyethylphosphonate dioxygenase and in follow up studies identified methylphosphonate from marine microbes as the most likely candidate culpable for methane levels at the ocean surface. A comprehensive understanding of the methane cycle and its role in oceanic life may help in regulating the greenhouse gas and understanding its importance above and below the waters. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues recently highlighted a PNAS publication, co-authored by Borden Lacy of Vanderbilt University. The authors describe a small molecule that targets Gram-positive bacteria and renders it photosensitive, suggesting that light treatment may help treat millions of Gram-positive skin and soft tissue infections. More on Tumblr.
Software Changes
ACEMD is now at version 20170619.
ADXV version 1.9.13 is now available.
ATSAS version 2.8.3 introduces datmw, a new program for unified access to multiple estimates of molecular weight and makes. This version also has updates to coral, dammif, datclass (with improved shape classification and new options to predict Dmax and MW from experimental data), a Molecular Weight wizard in primus/qt, saspy support for PyMOL 2.0, and a new option in sreflex to work with neutron data (SANS) along with improved performance with large structures.
BCFtools version 1.6 is now available with a new sort command, new consensus command options ( -i, --iupac option has been renamed to -I, --iupac, in favor of the standard -i, --include.), a +setGT plugin option to set genotypes based on a two-tailed binomial distribution test along with a new option to combine -i/-e with -t q, and added support for multiallelic sites and sex chromosomes in +mendelian.
cisTEM 1.0.0-beta is new to SBGrid. cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions. It includes a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.
CCP4 version 7.0.046 has new versions for DIALS and XIA2, updates to simbad in CCP4i that include a new interface and a sequence-free MR pipeline and containment search, and several bug fixes.
ChimeraX was updated to Alpha release 4/20171128. The developers have a steady stream of new features and bug fixes going out, detailed in this change log.
DIALS is now at version 1.8.1, the latest release. We got a couple of versions behind because of a bug in our alert system, which is now fixed.
Geneious version 11.0.4 includes mostly bug fixes and minor changes.
PEET version 1.11.1 was pushed out and includes an additional patch release. Since our last update you'll notice an update to MATLAB R2015b, the addition of meshInit and plotRotAxes, a change to save wedge weight MRC files by default, and fixes to a SIP compatibility issue on OS X, spikeInit handling of multiple objects, and modifyMotiveList ingoring flgInvert and flgEuler.
PHENIX was updated to version 1.13rc1-2961.
PyMOL version 2.0.6 is the new default. See the release notes for full details.
SAMtools version 1.6 is available with a new --output-qname option for mpileup, new markdup sub-command and -m option for fixmate, allowing users to mark and remove duplicates, and improvements to sort performance. Both sort and merge are now fully stable for all ordering options.
SBGrid Install Client GUI updates in the last quarter include user interface enhancements, new search features, improved command line admin flags, performance enhancements, better error detection, and a bevy of bug fixes. The latest version can be found at https://sbgrid.org/wiki/client_install.
SBGrid Website updates in the last quarter include new options to search software by developer name, software title, and keyword. You can also view a listing of software available by member type or license type and we've been doing lots of behind-the-scenes maintenance to improve documentation and optimize software distribution.
XDS version 20171218 now handles images obeying the definition of TIFF Revision 6.0.
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.