Dear Consortium Members and Affiliates,
As we greet these first days of fall we have some SBGRid news to pass along to you. Please read on for updates on our webinar series, a look at Gang Dong's group at the Max F. Perutz Laboratories, highlights from 3 member publications, 1 new member to welcome, changes to SBGrid MacOSX build platforms, and software changes: 5 application updates and 5 new software titles.
We had great turnouts for the Phenix/DivCon and HADDOCK webinars that were held in September. We just posted the Phenix/DivCon video on the SBGrid YouTube channel and we'll have HADDOCK up for you soon. Up next is a presentation on November 17th from DIALS developer Graeme Winter.
The focus of our September Webtale is Gang Dong, who described for us his scientific journey from China to the US (Texas then Connecticut) before landing in Austria. Now as group leader at the Max F. Perutz Laboratories at the University of Vienna, Dong's group focuses on understanding cilia and centriole assembly and their role in the survival of parasites that cause African sleeping sickness and malaria.
We have one new member to welcome for the month of September: Matthias Peter from ETH Zurich. Welcome Dr. Peter!
With MacOSX 10.10.5 solidly in place and the imminent release of 10.11 'El Capitan', SBGrid is moving the MacOSX build platform to 10.9 'Mavericks'. You may be wondering: Will my software still work on my 10.7 Mac? The answer: Yes, for now. SBGrid will continue to support software previously built for 10.7, and these old versions will run by default on this OS. These versions are often out-of-date, however, and will eventually become obsolete. Mac users should consider upgrading for performance enhancements and security fixes. The Linux build platform will remain CentOS 6.
In this month's software update we've got a handful of new software tools for you to explore. We pushed out updates to CCP4, DIALS, HKL200, Phenix, and RELION along with 5 new applications: iMODFit, Phenix/DivCon, rDOCK, summovie, and unblur. More details in the Software Changes section below.
A note about the new Phenix/DivCon tool: this plug-in requires Phenix ReadySet for protonation and fails due to a bug in Phenix 1.10. DivCon users should use the last Phenix release (1.9-1692) for ReadySet to work properly. A fix is forthcoming in Phenix, and we'll update SBGrid as soon as it is available.
For the month of September, SBGrid received two new citations in member publications, one from Lynne Howell at the University of Toronto in the Journal of Biological Chemistry J Biol Chem. 2015. 290:22827, and another in a PNAS publication from Thomas Schwartz's group at MIT PNAS. 2015. 112:E4975.
Over 77 manuscripts were published from SBGrid member labs last month. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- From the University of Chicago, Allan Drummond's Cell publication sheds new light on the impact of heat stress on proteins that aggregate, revealing that many proteins disassemble and return to a healthy functioning state after the cell returns to a normal temperature. Cell. 2015 Sep 10;162(6):1286-98.
- Roger Kornberg's group at Stanford U School of Medicine has an eLife publication describing the first 3-D model of the entire 21-subunit yeast Mediator complex using a combined approach relying on X-ray crystallography, homology modeling, and cryo-electron microscopy. Read the full story in Elife. 2015 Sep 24;4.
- From our undergraduate desk: students at Harvard Medical School will highlight a different member publication each month on our tumblr page. This month Kristen Rodrigues picked Peter Kwong's Nature Medicine paper describing efforts to make the influenza vaccine more effective. If you have undergraduate students that would like to choose a paper to highlight in future months, please have them contact Michelle Ottaviano.
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.
CCP4 version 6.5.017 was just pushed out and includes updates to coot, pointless, aimless, ccp4i, ccp4mg (adding ideal helices), and viewhkl.
DIALS is now at version dev-441 and you'll see a few bugs fixed.
HKL2000 was updated to version 708. This update includes support for Dectris Eiger detectors, increases in the scalepacklvirus limits, and now has a "no merge" original index option on the scale page.
iMODFit version 1.02 (Linux)/1.03 (OSX), one of our new titles from Pablo Chacon's group, is an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates. Check out the website for more on iMODFit.
Phenix version 1.10-2155 includes a bevy of bug fixes and new utilities, including CDL as the default protein restraint, tools for scaling/merging SAD data, a refactored xtriage GUI, use of intensities in molecular replacement, an occupancy refinement mode after MR, expanded real space refinement for cryo-EM/X-ray data, NCS constraints and improved rotamer fitting in refinement, improved and consolidated secondary structure restraints, validation of peptide planes, protein backbone validation using Cablam, TLS analysis tools, and a new continuous integration build system (BuildBot).
Phenix/DivCon version b2927 is new to SBGrid. This plug-in is a linear-scaling, semi-empirical quantum mechanics (SE-QM) program (DivCon) with the Phenix X-ray refinement engine. Phenix/DivCon does not utilize CIF(s), link restraints or other refinement parameters, so there are fewer assumptions about the model. Accurate energy and density scoring tools also allow tautomer/protomer and “flip state” determination.
rDock version 2013.1 - also new to the collection - is a fast, versatile program for docking ligands to proteins and nucleic acids. Check out the rDock website for more information.
RELION version 1.4 is the new default. With this update users have full classification and auto-refine capabilities for sub-tomogram averaging, focused classification with signal subtraction, 10x faster movie processing, more efficient threads implementation, and the option to compile in single-precisions, which saves 50% RAM.
summovie version 1.0.2 is our newest addition from Nikolaus Grigorieff's laboratory. summovie uses the alignment results from the software application unblur to calculate movie frame sums. What is unblur, you may ask?
unblur version 1.0.2 - the last of our new titles - is also from the Grigorieff lab. unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format and generates frame sums that can be used in subsequent image processing.
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.