Dear Consortium Members and Affiliates,
With the September launch of the academic season, SBGrid kicked into high gear and we have news on many fronts to pass along. Read on for more on an upcoming Phenix workshop, the PyMOLWiki transition to SBGrid, a PyMOL webinar online and a SITUS webinar scheduled for next week, a profile on U Wisconsin-Madison PI Brian Fox, a software release with 1 new title and 10 updates, a recommendation to hold off on Apple's latest OS release, two new members to welcome, and three member publication highlights.
We are excited to announce that SBGrid and NE-CAT will jointly host a Phenix workshop on experimental phasing, automated model building, and real space refinement, using cases from X-ray crystallography and electron microscopy. The workshop will be held on November 10-11 at Harvard Medical School in Boston. Take a look at the preliminary agenda and be sure to submit your application as soon as possible. Space is limited!
Earlier this month Jason Vertrees passed the PyMOLWiki reigns to SBGrid and we began managing and maintaining this resource. Many thanks to Jason, who spent over 10 years creating, building, and maintaining this site, with a significant investment of personal time and resources for the benefit of the community. Jason invited SBGrid to take over this endeavor, knowing that we are dedicated to facilitating access to software and training programs for structural biology. PyMOLWiki will remain free for all members of the scientific community.
PyMOL was also the focus of our webinar series in September and you can visit SBGrid's YouTube channel to view the September PyMOL webinar online. Don't forget to join us on Thursday to hear a presentation from Willy Wriggers on SITUS: Combining Structures from Different Biophysical Origins with Situs.
Brian Fox from the University of Wisconsin-Madison is the focus of our September member tale. Fox told us about his current work using automated technologies to characterize glycoside hydrolases, and gave us a little background on how these technologies, which act as a protein generating and structure-solving machine, were developed from Protein Structure Initiative-funded collaborations.
Our August software release includes one new software title - vlion - and updates to 10 applications, including autoPROC, BUSTER CCP4, DIALS, HKL2000, Phenix, PyRosetta, pysam (python module), Schrodinger, and Scipion.
Apple recently released macOS 10.12 Sierra for mac as a free upgrade. While this release is less substantial than the upgrade to 10.11 (El Capitan), we advise waiting for the next point release before upgrading production systems. We are not currently aware of major software incompatibilities with this OS version, but our testing to this point is limited. If you do upgrade and run into new problems, please report them to email@example.com.
In September two new members joined SBGrid: Luke Chao, from his new lab at Massachusetts General Hospital, and Niels Volkmann, our first member from the Sanford Burnham Presby Medical Discovery Institute. Welcome to our newest members!
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 6 new citations in member publications during the last month. Thanks to those who remembered us, including Thomas Schwartz from MIT in two publications Elife. 2016 Aug 4;5. pii: e17983
and Sci Signal. 2016. 9(446):ra92, SUNY Upstate's Michael Cosgrove in J Biol Chem. 2016 Aug 25, Andrew Kruse at Harvard Medical School Structure. 2016 Sep 7. pii: S0969-2126:30229-5,
Lokesh Gakhar from the University of Iowa, PLoS Genet. 2016.12:e1006287, and La Trobe University's Marc Kvansakul PNAS. 2016 Sep 19. pii: 201607855
Over 80 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:
- Phoebe Rice's group at the University of Chicago examined the crystal structure of intact Cch, a conserved protein encoded by SCC, revealing a ring-shaped architecture and providing evidence that SCC elements can replicate. Read more in Nat Struct Mol Biol. 2016 Aug 29.
- At Stanford University School of Medicine, Roger Kornberg's group used cryo-EM and chemical cross-linking to assemble and determine the complete Mediator-PIC complex, a 52-protein, 2.5 MDa Mediator-RNA polymerase II initiation complex. Read the full story in Cell.
- From our undergraduate desk: Harvard student Kristen Rodrigues highlights a paper in Nature from SBGrid members Daniel Kahne, Suzanne Walker, and Andrew Kruse of Harvard Medical School that examines the role of the SEDS family of proteins in bacterial cell wall formation. Read more on Tumblr.
In BUSTER version 20160923 we've got some new goodies in the form of a -h5master input option in Pipedream to allow Pipedream to run with input Eiger HDF5 data, a fix to the water addition procedure to ignore existing hydrogen atoms, and updates to PTR (O-PHOSPHOTYROSINE) restraints along with a number of other improvements.
In CCP4 version 7.0.020 you'll find that pisa now writes crystal data in output structure files, ccp4i2 allows the optional use of a native file browser, there is added support for nucleic acids in prosmart, a correction to the pyrogen python call in coot, and updates to pointless and ARP/wARP.
DIALS was updated to development version 20160926.
HKL2000 version 714 includes a new version of the frame display program XDisp Qt that can be accessed from the 'Options' menu, initial support for h5 files for Pilatus and Eiger detectors, added support for the Rayonix MX300HE and Stoe pad200k formats, and an update to the Pilatus “read header” procedure and the “split data sets” window.
Phenix is now at version 1.11rc3-2542.
PyRosetta was updated to version 20160901.
The pysam python module was updated to version 0.9.1.4
In Schrödinger version 2016-3 you'll get a chance to beta-test Maestro 11 and provide feedback. Learn more about the Maestro 11 beta at https://www.schrodinger.com/maestro11.
Scipion version 1.0.1 (Linux only) includes bug fixes and improvements to several protocols (Spider, Xmipp, Frealign output, summovie and unblur movie alignment, Relion, and Resmap) and several fixes for Picking and Viewer.
vlion version 20160314 (Linux only) is new to SBGrid. Vlion is a slightly vectorized version of the original RELION 1.4 code by Dmitry Tegunov of the Max Planck Institute.
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.