Dear Consortium Members and Affiliates,
As we round the corner from January into February I begin to notice the lengthening days and now look ahead with hope to fewer dark hours. Light or dark, SBGrid chugs along with a new Ambassador Program, an upcoming February webinar along with 2 from January available on YouTube, a member tale on U Chicago's Phoebe Rice, a software release with 14 updates and 6 new applications, 12 new members to welcome, and 3 member publication highlights.
Last week we announced plans for the SBGrid Ambassador Program and are currently accepting applications from those who would like to participate in this global forum to help steer the development of SBGrid. Represent your fellow laboratory, departmental, or institutional scientists to help us identify computing challenges and address unmet needs of the community. Read the full details and contact Michelle by Feb 28th to apply.
Our February webinar will feature OpenMM with Peter Eastman presenting from Vijay Pande's lab at Stanford University. OpenMM is a toolkit for molecular simulation that combines extreme flexibility with high performance. Our January webinars, which focused on xfel processing tools, are now posted on YouTube channel. If you missed either of these, you can watch the videos for cctbx.xfel or Iota and Prime now.
Read our February member tale for an interesting cocktail party conversation starter, from Phoebe Rice at the University of Chicago, and insight into this linguistics student turned structural biologist's work on MRSA and the mobile element that carries it.
We pushed out a big software release this month, including updates to AutoProc, Buster, DIALS, EMAN2, GCTF, Phenix, Phenix/DivCon, Priism/IVE, pysam, R, Relion, SHARP, VMD, and XDS. We also added 6 new applications: BiopTools, POMONA, PowerFit, RNA Framework, SPHIRE, and STRIDE.
January brought us 12 new members from around the world, including Alexandra Deaconescu at Brown University, Jacqueline Cherfils of École Normale Supérieure in France, Zbyszek Otwinowski and Youxing Jian at University of Texas Southwestern Medical Center, Susan Shao of Harvard Medical School, Yi Ren at Vanderbilt University, Kuo-Chiang Hsia, Chwen-Deng Hsiao, and Hanna Yuan from Academia Sinica in Taiwan, Kay Diederichs of Universität Konstanz, and Michael Ragusa and Dean Madden from Dartmouth College. It was exciting to see so many new faces from so many different places. 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, from Rockefeller's Roderick MacKinnon in Cell, the Institute of Structural Biology's Dirk Niessing in Nature Structural and Molecular Biology, University of Toronto's Oliver Ernst in Structure, La Trobe University's Marc Kvansakul in the Journal of Virology and Cell Death and Disease, and Washington University School of Medicine's Thomas Brett in eLife.
Over 80 publications from SBGrid member laboratories appeared in our December search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Appearing in Science is an article from Emil Pai's group at the University of Toronto which identifies the asymmetry in the two protomers of the homodimeric enzyme fluoroacetate dehalogenase, where only one protomer is able to bind substrate at any given time. [Abstract]
- Leemor Joshua-Tor's group at Cold Spring Harbor Laboratory describes the structure of the Origin Recognition Complex published in eLife [Article]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a paper in Nature Structural & Molecular Biology from SBGrid member Weikai Li's group at University of Washington School of Medicine, reveals that warfarin, a commonly-used anti-coagulant drug, acts on a cellular level to prevent an electron-transfer step in hVKOR. [More on Tumblr].
AutoProc version 20161207 includes an update to GPX2, which now automatically detects and loads image files compressed with either gzip for bzip2 along with a number of other bug fixes and improvements.
BiopTools version 1.2 was added from Andrew Martin's group. BiopTools is a set of command line tools written in C and that make use of the BiopLib library to manipulate protein structure and sequence.
BUSTER version 20161207 improves output for grade_PDB_ligand, implements fixes in REMARK 3, introduces an option to to keep all waters present in input file, and makes general usability improvements.
EMAN2's nightly release 20170110 was added.
DIALS version 1.4.1 includes a few bug fixes and the new command dials.two_theta_offset, which givves the offset of the two theta axis given two experiment .jsons.
GCTF was updated to version 1.06.
Phenix is now at development version 2645. Since our last update the developers have introduced improvements to geometry restraints, the NCS search, phenix.real_space_refine, model, Phaser, validation, geometry, and support for Amber. There area also new map and model-building tools and a simplified Rosetta installation.
The Phenix/DivCon plugin was updated to version 7.1.1-b4015.17.
POMONA is new to SBGrid. POMONA is a newly designed NMR chemical shift guided protein structure alignment method to generate protein templates with the best matched local structure from the PDB.
PowerFit 20170123 was also added to SBGrid. PowerFit is a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities, from Alexandre Bonvin's group,
The pysam python module was updated to version 0.10.0.
R was updated to version 3.3.2 (code name: Fire Safety).
RELION version 2.0.2beta is now available. The last stable release, 1.4, is the default version, but 2.0.2beta can be accessed by version override.
Also new is RNA Framework 20170111. RNA Framework from Danny Incarnato, which supersedes RSF, is a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data.
SHARP is now at version 20161207, which includes a new flag "-pdbkeep" that uses the input PDB file to find and refining heavy-atom sites. It also uses the phase information from that model during phase computation.
SPHIRE is new to SBGrid for Linux at version 20161216. SPHIRE is designed for easy access to Cryo-electron microscopy with the clear goal of quality assessment and result reproducibility by statistical resampling.
Stride, too, is new to SBGrid. From developer Dmitrij Frishman, Stride is a program to recognize secondary structural elements in proteins from their atomic coordinates.
VMD version 1.9.3 includes the new QuikMD plugin that connects VMD and NAMD and allows users to prepare common molecular simulations in just a few minutes. Also new is the Force Field Toolkit plugin to develop CHARMM-compatible (e.g., CGenFF) force field parameters.
in XDS version 20161205 the developers fine-tuned the determination of low background for estimating reflection intensities in the INTEGRATE step and fixed a few other bugs.
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.