Dear Consortium Members and Affiliates,
With our final newsletter of 2015 we send our wishes to all for Happy Holidays and perhaps even for a bit of snow for those of us in Boston. Our December news includes a reminder about our holiday schedule, a new webinar to watch online along with webinar plans for January, details on the next SBGrid-Schrodinger Working Group meeting, a profile on Enrico Di Cera from St. Louis University, a software release including 12 updates, one new member to welcome, and three member publications to highlight.
Harvard Medical School and SBGrid staff will be on holiday starting December 24th, but will be back in business on January 4th. During the break we'll keep an eye out for emergencies, but the small stuff will stay on hold until the new year. Happy Holidays to all!
We recently hosted a special seminar featuring Filipe Maia from Uppsala University, who spoke about SPI at XFEL's and the birth of SFX. This was a local, live presentation, but the recorded version is now on SBGridTV. Watch here. We'll host the next webinar in this series on January 26th with a presentation from Roberto Terero on PDBStat.
Our SBGrid-Schrodinger Working Group will connect for a 3rd meeting on Tuesday, January 12th. Woody Sherman, Vice President and Scientist at Schrodinger, will join us again to give a presentation on the "Role of water molecules in protein preparation, docking, and scoring". Reminders will go out through the Working Group mailing list, so please be sure to email Michelle Ottaviano if you have not yet joined this group.
Enrico Di Cera from St. Louis University shared some of his story with us for our December Tale. He describes his work on prothrombin and thrombin and it's potential as a blood coagulant. Di Cera also emphasizes his view of structural biology as a tool to complement his research, noting “Pretty pictures make you feel good; Solid biochemistry makes you feel right.”
This month's software release includes updates to autoPROC, Buster, DIALS, EMAN2, EPMR, FASTA, ImageMagick, MCCE, NMRPipe, Phenix, PyMOL, and Simulaid.
Take a look at our job postings page for opportunities at University of California, San Diego, Dana-Farber Cancer Institute, and right here at SBGrid. We recently updated our posting for a Lead Senior Research Data Management System Developer. Full details here.
SBGrid's newest member is Rick Stegeman from Washington University St Louis. Welcome!
For the month of November, SBGrid received 2 new citations in member publications. Katya Heldwein, from Tuft's University School of Medicine, gave us a nod in her article on membrane budding in herpesvirus capsids EMBO J 2015 34:2921-36, as did Evris Gavathiotis from Albert Einstein College of Medicine, in his publication on BAX inhibition J Biol Chem.
Over 20 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:
- Appearing in PLOSOne from Pär Nordlund's group at the Nanyang Technological University in Singapore, is a study that shows that herpesvirus VZV encodes to thymidylate synthase, which in turn binds an activated herpesviral drug BVDU, offering new potential for more specific VZV inhibitors. PLoS One. 2015 10:e0143947.
- Katherine Henzler-Wildman's recent study, published in PNAS, describes transmembrane allosteric communication in the small bacterial channel NaK that was unexpected and has significant implications for understanding channel function. PNAS 2015 112:15366-15371.
- From our undergraduate desk: Harvard Medical School student Kristen Rodrigues chose to highlight an article that appeared in the journal Proteins, from Ivan Rayment's group at the University of Wisconsin, which describes how they computationally cobbled together 5 sections of the coiled-coil that make up the myosin rod, with a hope to use this method to model the complete myosin rod. Read more here.
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data along with the PDB record and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
autoPROC version 1.0.3 includes a new option to create early/late data values, new support for RIGAKU/Eiger detectors, and a reworking of the feature that automatically selects a subset of images for spot searching along with a number of other bug fixes and improvements.
BUSTER version 20151214 was pushed out. This version includes a major reworking of geometry checks, new support for computing and analyzing anomalous Fourier maps, and performance improvements in many stages.
DIALS nightly build dev-496 is the new default.
EMAN2 was updated to the nightly release 20151210. This update includes the new sxrelion2sparx.py, which should be able to handle the star file from any processing stage. This version is available via a version override.
EPMR has been updated to version 15.12.
FASTA version 36.3.8b extends alignment sub-scoring scripts to allow overlapping domains, which requires a modified annotation file format and new annotations scripts, which available in the fasta-36.3.8/scripts directory.
ImageMagick is now at version 6.9.2-4 for Linux/6.9.1 for OS X.
MCCE version 2.7 is now available.
NMRPipe version 20151124 was pushed out.
Phenix nightly build dev 2229 is now available as a version override.
PyMOL is now at version 22.214.171.124. This version includes improved mae support and fixes stick and sphere rendering issues on OS X with ATI Radeon R9 graphics cards. It also finalizes support for CIF/mmCIF
Simulaid is now at version 20150910.
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.