Dear Consortium Members and Affiliates,
As we get ready to leap into May, we have some SBGrid news to pass along, including an update to our webinar lineup, a profile on scientist/programmer James Holton, a software release with ten updates and two new titles, positions postings for NE-CAT and Dana-Farber Cancer Institute, two new members to welcome, and three SBGrid member publication highlights.
Many thanks to Tom Goddard, who gave us a great preview of ChimeraX in our April webinar. We've uploaded the ChimeraX recording to SBGridTV for those who missed it or want to watch again. May brings a presentation from Andrew Orry on ICM-Browser-Pro for 3D Molecular Graphics and Protein Structure Analysis, and our lineup for the summer and fall includes Dock, BioXTAS RAW, SPHIRE, and EMAN2. Be sure to join us online.
We caught up with James Holton, Beamline Scientist at the ALS in the Lawrence Berkeley National Laboratory, for our April web tale. Holton described his passion for biology, his work alongside Tom Alber to develop Elves, and his current effort to develop MLFSOM, a tool to identify the source of errors when collecting X-ray data. Read the full Tale.
Our April software release includes updates to BioXTASRAW, CCP4, DIALS, Gromacs, HKL2000, Hole, IMOD, ORCA, Phenix, and Relion, We've also added a pre-release of the much anticipated ChimeraX and MGLTools2.
We're passing along information on position postings from NE-CAT and Dana Farber Cancer Institute:
- NE-CAT, at Cornell University is looking for a postdoc in macromolecular crystallographic computing who will work on developing, disseminating, and supporting RAPD. Full job posting
- Wayne Maraco's laboratory in the Department of Cancer Immunology and Virology at the Dana-Farber Cancer Institute is seeking a Senior Fellow or an entry level Scientist with training in structural biology. Full job posting.
Two new members joined SBGrid in the month of April: Deena Oren from Rockefeller University and Yves Bourne from the Architecture et Fonction des Macromolécules Biologiques laboratory in Marseille, France. 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 4 new citations during the last month, a nod from Thomas Schwartz's MIT lab in EMBO Reports [Abstract] and Brandt Eichman's lab at Vanderbilt in PNAS [Abstract], and a referencein a Journal of Biological Chemistry article from Marc Kvansakul's group at La Trobe University and a Nature Communications publication from Juan Fontecilla-Camps's group at the Institut de Biologie Structurale [Abstract]
Over 60 publications from SBGrid member laboratories appeared in our latest monthly search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- From Chris Hill and Wes Sundquist at the University of Utah, we learn a bit about Vps4-Vta1 AAA ATPase protein translocation from 4.3 Å cryo-EM structure. [PDF]
- Jose Maria Carazo's group at Centro Nacional de Biotecnología describe a technique - XTEND - for cryo soft X-ray tomography to increase the depth of field to study thick specimens more accurately. [Article]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a paper that appeared in Cell, from SBGrid members Allan Drummond and Tobin Sosnick at the University of Chicago, which describes how the poly(A)-binding protein acts as a senses stress and phase separates in response. [More on Tumblr].
BioXTASRAW version 1.2.2 is the new default. This version includes several useful new features. RAW now has the ability to do weighted averages of scattering profiles, is now compatible with ATSAS version 2.8.0, allows the user to run DAMMIN from RAW, and can now handle files with multiple images (though this work is still in the early stages).
ChimeraX is new to SBGrid. ChimeraX, currently an alpha product, is a next-generation molecular visualization program, following UCSF Chimera. Compared to Chimera, ChimeraX has better graphics (e.g., interactive ambient shadows), handles large structures (millions of atoms) much faster, and has a more modern, single-window user interface. ChimeraX will have documented programming interfaces and an easy-to-use “Tool Shed” web repository of extensions.
CCP4 version 7.0.036 was pushed out with updates to pointless, aimlesss, ctruncate, and pisa.
DIALS version 1.5.1 release notes are available on the website.
GROMACS release 2016-3 was pushed out, enabling set GMX_SIMD=None by default on architectures that allow it and introducing a work around for OpenMPI 2 test failures. The last stable releases (4.6 Mac/5.1.2 Linux) are still the defaults.
HKL2000 version 715 introduces more efficient processing of the NeXus .h5 data, support for new detector formats (Rigaku PAD4M and Oxford Atlas, Rayonix mx170hs and Pilatus 1M), and improvements in the scaling, integration, and reporting.
Hole version 2.2.005 is the new default. With this updated verion, Hole has transitioned to Open Source software and is now freely available to all users.
IMOD is now at version 4.9.2. The jump to 4.9 brought major functional enhancements including use of fiducial markers to automatically register between dual-axis tomograms, use of local patch correlations to automatically increase patch size, new programs to detect the surfaces of the specimen in a tomogram, improvements to Batchruntomo to build a dual-axis tomogram automatically, and a new program to align frames from a direct detector camera.
MGLTools2 version 1.0 is new to SBGrid. MGLTools2 is a collection of software tools for docking flexible ligands into receptors with selective flexibility: AutoDockFR: a docking engine using the AutoDock4 forcefield; AutoGridFR: a graphical user interface for setting up docking boxes; AutoSite: a ligand binding site detection and characterization program.
ORCA was bumped up to version 4.0.0. A detailed listing of new features is shown on the website.
Phenix development version 2747 is now available.
Relion was updated to version 2.0.4.
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.