Dear Consortium Members and Affiliates,
As we bid adieu to June, we welcome summer and your participation in next week's Schrodinger Working Group and in our Data Bank project. We also remind you to join our regular monthly webinar featuring CrystFEL, invite you to read about SBGrid member PI Julie Forman-Kay, update you on our WSMR portal, announce four new members, describe our recent software release with 9 updates and 1 new application, and highlight publications from 3 member laboratories.
We'll hold our first Schrodinger Data Club/Training working group next Tuesday at 12:00pm EDT for all non-profit groups in North America and Australia that are using the Small Molecule Suite. Participation in the work group is necessary for any groups wishing to access this software, so if you haven't signed up yet, please complete our our Google Form now.
As we continue to develop the SBGrid Data Bank for x-ray diffraction data sets, we'd like to ask for your support once again. We are submitting a grant in the coming days to an agency that has expressed a strong interest in extending our infrastructure development. It will be important for us to show that our community is actively using this system to deposit datasets for historical and upcoming publications. If you have a paper in the works, you can deposit your dataset now and put it "on hold" until the date of publication. Visit us at https://data.sbgrid.org to upload your datasets and many thanks for your continued support!
In our July webinar we're looking at some new-fangled technology with CrystFEL developer Thomas White. Join us July 14th at 12pm to learn more about this application, which processes diffraction data obtained using Serial Femtosecond Crystallography (SFX) with a free-electron laser source.
Julie Forman-Kay, from the Hospital for Sick Children, University of Toronto, is the focus of our June webtale. Forman-Kay likes a dash of disorder with her science and has spent much of her scientific career seeking to understanding the function of disorder in protein dynamics. Read more about her science on the Member Tales section of our website.
We recently finished rebuilding the submission node for our Wide Search Molecular Replacement (WSMR) portal and are now working through the jobs that got backlogged during the rebuilding process. If you have a pending job that is urgent, please contact us at firstname.lastname@example.org and Mick or one of our other Portal Team members will try to re-prioritize your job. WSMR is available at https://portal.sbgrid.org/.
Four new members joined SBGrid in June: Jay Chodaparambil from Biogen, Peter Sorger from Harvard Medical School's Systems Biology department, Eduardo Perozo became our 12th member at U Chicago, and with Alejandro Buschiazzo from the Institute Pasteur de Montevideo, we now have a dot on the South American map. Welcome to our new members!
Our June software push includes updates to adxv, ALBULA, AmberTools, AUTO3DEM, Geneious, ilastik, iMosflm, Phenix, and XDS, and one new software application: DireX. Read details about the updates below.
SBGrid member labs published over 80 manuscripts during the last month, a full listing of which can be found on the Member Publications page of the SBGrid website. Here are some notable highlights:
- From Jennifer Doudna's laboratory at UC Berkeley comes a publication in Science that gives us new information on Cas9- guide RNA binding.
- Also in Science is a publication from Bing Chen's group at Boston Children's Hospital, which describes two conformationally homogeneous trimeric HIV-1 envelopes, helping to build a better picture of an untriggered HIV-1 envelope.
- Ming Zhou's group at Baylor College of Medicine report on their crystal structure of mouse SCD1 bound to stearoyl-CoA in the June 22nd edition of Nature.
If you have news from your lab that you would like to share with the community, please let us know by emailing Michelle Ottaviano or communicating with SBGrid on Twitter (@SBGrid).
adxv version 1.9.10 is the new default. No release notes are available.
ALBULA is now at version 3.0.0-14. This version combines the detector, image, and beamline information in the raw header, displays images via drag and drop, exports images and screenshots to png and jpeg, and makes a number of improvements to ROI including options to copy to clipboard, pop out, and log mode, improved display, normalized values in Box Plot, and an option to set the beam center in Powder Plot.
AmberTools was updated to version 14. This version includes improvements and bug fixes to many tools. Included are improved simulations workflows, expanded cpptraj functionality with support for the Grid Inhomogenous Solvent Theory (GIST) and hydrogen mass repartitioning in ParmEd, an option for semi-empirical Born-Oppenheimer molecular dynamics (SEBOMD), multi-dimensional Replica Exchange molecular dynamics in sander, pmemd, and pmemd.cuda, new analysis tools for crystal lattice simulations, and improved support of CHARMM force fields and VMD-generated topology files using chamber.
The AUTO3DEM update to version 4.05 includes a number of bug fixes and performance improvements. Some noteworthy changes include new support for the gold standard procedure and Mac platforms, an option to visualize large maps in RobEM, and a function in autopp for preprocessing stacks of particles that can avoid masking box corners (options B, F and O) and delete the input stacks immediately after generating the processed stack (options F and O).
DireX version 0.7.0 is new to SBGrid. From Gunnar Schroeder's group at the Institute of Complex Systems, Forschungszentrum Jülich, DireX performs efficient geometry-based conformational sampling of protein structures by combining prior structural information with experimental data through the Deformable Elastic Network (DEN) approach.
Geneious is now at version 7.1.9 (from version 7.1.7). With this update you'll see bug fixes, a change to the XML display format for E-Utilities/ESummary in the NCBI Gene Database, an option to edit documents from future versions of Geneious, and a correction that prevents users from selecting invalid Salt Concentration options.
With version 1.1.5, ilastik has made an major overhaul from the back-end to the user interface. Pixel classification is no longer limited by the RAM of your machine and, when Carving, all objects are now segmented separately, making for much faster saves and smaller project files. New workflows include Object Classification, Tracking, with an automatic tracking option, that implements the Conservation tracking algorithm to track multiple dividing objects, along with an option for manual tracking, and Counting, which allows you to count objects in crowded scenes without performing segmentation or object detection.
iMosflm is now at version 7.2.0. In addition to bug fixes and other improvements, this version includes a "known cell" indexing option, the ability to display images in "reverse video", an option to process images collected with the ADSC Pixel Array Detector at APS and with Dectris Eiger 4M images collected at ESRF, and no longer requires the user to set the environment variable MOSFLM_EXEC.
Phenix nightly build dev-2067 was added to the tree. No details for this release are shown on the Phenix website.
XDS version 20150617 includes improved determination of the integration region of diffraction spots recorded at large detector distances and short wavelengths. Also, XSCALE now lists incompatible data sets or those lacking overlap with the main set.
Please don't forget to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
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.