Dear Consortium Members and Affiliates,
Our January newsletter comes to you from Boston, all cranky and cold and hoping to thaw as temperatures finally rise above freezing. Those of you to our north will surely sigh and roll your eyes, but...brrrrrrrr. Frozen fingers aside, we have some interesting news to share, with a a date for the next SBGrid Computing School, new tutorials exploring crystallization techniques, an HKL2000 webinar next week, a little history on Graeme Winter and xia2, and a software update that includes two new packages.
We've just set the date for our annual computing school, which we will host in conjunction with NE-CAT on June 4-6, 2104. Quo Vadis Structural Biology 2014? will be held in Boston on the Harvard Medical School campus and will focus on data processing in crystallography. Kay Diederichs will be one of the key presenters, and we are currently finalizing the program details with a plan to publish the details in our next newsletter. Please save the date!
The main software update for January was distributed Thursday evening and included new versions of PyMOL, CCP4mg, Xplor-NIH, HKL2000, Gnuplot, XDS, MAFFT, and a PHENIX nightly release as well as the latest CCP4 bug fixes and two new packages: autoPROC and TALOS-N.
Three short tutorials that focus on "Simple Ways to Enhance the Success of Crystallization Trials" were recently posted to the SBGridTV YouTube channel. Many thanks to Naomi Chayen for developing these presentations and sharing her time and expertise. Her lab at Imperial College London focuses primarily on understanding the crystallization process and developing improved methods.
Wladek Minor will give us an update on the future of HKL-2000/HKL-3000 next Thursday. Please be sure to join his webinar on February 6th at 11:00am EST. Also on the horizon are webinars on SAXS techniques, Gorgon, a cryo-EM molecular modeling application, and Phenix-Rosetta refinement. More details to follow.
Some of you may have tuned in to find us facing technical difficulties during the REDCAT webinar that was held in December. If you were unable to stay connected for the presentation, the REDCAT video has now been posted. Please pay a visit to SBGridTV to watch.
We're turning our focus to developers in this month's SBGrid Tale, with a look at Graeme Winter and the development of xia2. Read about how this astrophysics student found himself working at the UK's Diamond Light Source and his continued efforts to improve the way data processing software handles today's more subtle and sophisticated data sets.
Four new members have joined the Consortium this month. Danesh Moazed is our newest from Harvard Medical School and Johns Hopkins University School of Medicine has joined the SBGrid ranks, represented by James Berger, Herschel Wade, and Cynthia Wolberger. Welcome to our new members!
Software Update
Linux 64-bit and OS X Intel
PyMOL has been updated to version 1.7. There is a list of new features and the incredible PyMOL Wiki with details and documentation on how to use the software.
CCP4mg has been updated to version 2.8.1. The CCP4mg changelog has notes on the bugs fixed in this release and the many new features introduced in the 2.8.0 release. There is comprehensive documentation for using the movie-making and figure preparation tools in CCP4mg.
Xplor-NIH has been updated to version 2.35. This release has extensive new features and bugfixes from the 2.34 release, which are exhaustively documented in the change log.
TALOS-N is a new package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts. TALOS-N uses an artificial neural network (ANN) based hybrid system for empirical prediction of protein backbone φ/ψ torsion angles, sidechain χ1 torsion angles and secondary structure using a combination of six kinds (HN, Hα, Cα, Cβ, CO, N) of chemical shift assignments for a given residue sequence. More details are available on the TALOS-N home page.
autoPROC from Global Phasing is a new addition to the supported software list. This software requires licensing on a per-user basis, and you will need to acquire a license from Global Phasing in order to use it. Once you have a license file, you can copy it to /programs/local/autoproc/autoproc_licence and the software will start working. Documentation for the software as well as the license request form can be found on the autoPROC website.
HKL2000 has been updated to version 704y. The HKL release notes mention some bug fixes and new features.
PHENIX nightly release dev-1593 has been added to the software tree. Phenix-Rosetta refinement should be working somewhat better on OS X now. The changelog and documentation are available on the PHENIX website.
CCP4 patch 7 has been installed. The CCP4 updates page has a list of fixed bugs.
MAFFT has been updated to version 7.130. This release contains mostly bugfixes as noted in the MAFFT changelog.
The XDS data processing tool for X-ray crystallography has been updated to version 20140110. The XDS release notes contain details on the changes.
Gnuplot has been updated to version 4.6.4. This tool is used for plotting output data from many of the scientific applications in the software. The release announcement is on the Gnuplot website.
Publications
Please cite eLife 2013;2:e01456 for all projects completed with SBGrid compiled software. Since our last newsletter, the following publications have appeared from Consortium member labs:
- Ban Lab, ETH Zurich: Architecture of the large subunit of the mammalian mitochondrial ribosome.
- Chen Lab, Children's Hospital Boston:
- The ABC-F protein EttA gates ribosome entry into the translation elongation cycle.
- EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics.
- Drennan Lab, MIT: Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism.
- Eichman Lab, The substrate binding interface of alkylpurine DNA glycosylase AlkD.
- Ernst Lab, University of Toronto: Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms.
- Heras Lab, La Trobe U: The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping.
- Ikura Lab, U Toronto: STIM1/Orai1 coiled-coil interplay in the regulation of store-operated calcium entry.
- McGlade Lab, Hospital for Sick Children: The ubiquitin ligase RNF126 regulates the retrograde sorting of the cation-independent mannose 6-phosphate receptor.
- Nilges Lab, Institute Pasteur: SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes.
- Nordlund Lab, Nanyang Technological U: Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell.
- Piper Lab, U Iowa: Backbone and side-chain NMR assignments for the C-terminal domain of mammalian Vps28.
- Rees Lab, Caltech: Turnover-Dependent Inactivation of the Nitrogenase MoFe-Protein at High pH.
- Shamoo Lab, Rice U: Adaptation of Enterococcus faecalis to Daptomycin Reveals an Ordered Progression to Resistance.
- Singh Lab, Yale School of Medicine: Radioligand Binding to Nanodisc-Reconstituted Membrane Transporters Assessed by the Scintillation Proximity Assay.
- Skiniotis Lab, U Michigan: Characterization of a Highly Flexible Self-Assembling Protein System Designed to Form Nano Cages.
- Springer Lab, Children's Hospital, Boston: Highly reinforced structure of a C-terminal dimerization domain in von Willebrand factor
- Stone Lab, Vanderbilt U: Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence.
- Wagner Lab, Harvard Medical School: The Interaction between Eukaryotic Initiation Factor 1A and eIF5 Retains eIF1 within Scanning Preinitiation Complexes.
- Walensky Lab, Dana-Farber Cancer Institute: Mantle Cell Lymphoma in Cyclin D1 Transgenic Mice with Bim- deficient B-cells.
- Zheng Lab, U Washington:
- D14-SCFD3-dependent degradation of D53 regulates strigolactone signalling.
- Structural basis for Ca2+ selectivity of a voltage-gated calcium channel.
For the full list of publications please visit the publication section on the SBGrid website.
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.