Dear Consortium Members and Affiliates,
With this Halloween edition of the SBGrid newsletter, we've included a few of EM treats for you, with a profile on Sjors Scheres, a RELION 3.0 webinar, and the addition of CCP-EM to our software tree. In other news we have a software release with 9 updates and 4 additional new titles, a new position posting at Harvard Medical School, 12 new members to welcome, and 3 member publication highlights.
For our October SBGrid Tale, we caught up with Sjors Scheres, of RELION fame, to get a glimpse at the path he followed to develop this tool, learn about the newest features in RELION 3.0, and look at his scientific endeavors in the wet-lab, collaborating with neuroscientist Michel Goedert to examine tau filaments in the brain. Read the full story.
In keeping with our theme, next up in our webinar series is a much-anticipated presentation from Sjors Scheres on RELION-3: new tools for automated high-resolution cryo-EM structure determination. Join us Nov 6 at 12pm EST - details here. In case you missed the presentation from Lance Westerhoff on Phenix/DivCon a few weeks ago, hop on over to our YouTube channel to watch online.
Our October software update includes new versions of AmberTools, CCP4, Chimera, crYOLO, Geneious, IMOD, PHENIX, Pysam, and SCIPION, and 5 new applications: HHsuite, Jupyter Notebook, JupyterLab, plmc, and the long-awaited CCP-EM.
New this month on our position postings page is a listing for a Cryo-EM Specialist at the Harvard Cryo-EM Center for Structural Biology. Check out this posting and others from SBGrid member labs on our website.
October also brought us 12 new members and a couple of transplants to new institutes, with Charles Weitz joining from Harvard Medical School, Jonathan Shu from Cornell University, and Anshul Bhardwaj from Thomas Jefferson University. Carsten Sachse is setting up shop at Forschungszentrum Jülich, and Daniel Panne made the move to Leicester University, introducing SBGrid to a few of his new colleagues: John Schwabe, Peter Moody,Thomas Schalch, Mark Carr, Cyril Dominguez, Alfredo De Biasio, Russell Wallis, Bibek Gooptu, Geerten Vuister. 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 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.
Four new citations appeared for SBGrid's eLife paper in October. Thanks to those who remembered to acknowledge us, including Douglas Rees of California Institute of Technology in PNAS [Abstract]; Seth Darst from The Rockefeller University in Nature Communications [Abstract]; MIT's Catherine Drennan in eLife [Abstract]; and EMBL Grenoble's Stephen Cusack in Nature Communications [Abstract]
Over 30 member publications appeared in journals this month. You can find a complete listing on our website, along with a few notable highlights below:
- In Journal of Biological Chemistry, Cynthia Wolberger of Johns Hopkins University School of Medicine determined the role of OTUB1 in protecting UBE2E1 from degradation by thwarting E2 autoubiquitination activity. [Abstract]
- Brandt Eichman of Vanderbilt University has a new publication in International Journal of Molecular Sciences where he reported that a conserved loop within the translocation in the RecG (TRG) motif is necessary to activate DNA replication fork reversal. This work continues the effort to elucidate the players involved in the DNA fork binding, reversal, and progression that is essential for accurate DNA replication. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a Nature publication from Matthias Wolf's group at the Okinawa Institute of Science and Technology in which they report on the use of single-particle cryo-electron microscopy visualize the Ebola virus nucleoprotein-RNA complex at near-atomic resolution More on Tumblr.
AmberTools 18 is out. This version includes a CUDA-enabled pbsa solver; extensions for membrane modeling with PB, a lambda-dynamics method for constant pH simulations, the packmol_memgen tool for building lipids and bilayers, a new ("middle") integration algorithms in sander, build tools based on CMake, and continued updates and extensions to cpptraj to allow users to obtain energies from snapshots of PME simulations along with improved scripting abilities.
CCP-EM version 1.1.0 is finally available to SBGrid members! CCP-EM is a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to a various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.
CCP4 version 7.0.065 is now available.
Chimera version 1.13 has a new serial-numbering option for saving very large PDB files, a Tools menu to access third-party plugins, notably the Tangram suite of molecular modeling tools from InsiliChem, an update to the Dunbrack backbone-dependent rotamer library, several new command options, and a number of bug fixes.
crYOLO was bumped a few releases version 1.1.4, which includes a number of performance improvements and bug fixes.
Geneious is now at version 11.1.5.
HHSuite 3.0.3 is new to SBGrid. HHSuite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
IMOD 4.9.10 includes fixes to Ctfphaseflip, Excise, Boxstartend, and the sphere radius output from imod2vrml2.
Jupyter 4.4.0 was just added to SBGrid. Jupyter is a language-agnostic HTML notebook application for Project Jupyter.
JupyterLab 0.35.2 is also new to the collection. JupyterLab is the next-generation web-based user interface for Project Jupyter, which enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.
PHENIX version 1.14-3260 includes new and reorganized tools for cryo-EM tools, bug fixes and improved data information content functionality in Phaser. In Ligands, you'll find better support for metals and metal clusters and added support for the QM package, Orca. You'll also notice improved performance for NCS search, generating secondary structure restraints, and clashscore calculations
plmc 20171002 is a new addition to SBGrid. plmc infers undirected graphical models to describe coevolution and covariation in families of biological sequences. With a multiple sequence alignment as an input, plmc can quantify inferred coupling strengths between all pairs of positions (couplingsfile output) or infer a generative model of the sequences for predicting the effects of mutations or designing new sequences (paramfile output).
pysam was bumped a few versions to 0.15.0
SCIPION is now at version 1.2.1.
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.