Dear Consortium Members and Affiliates,
October brings big news for SBGrid, with the launch of our long-awaited workstation software installer available to all member labs for Mac and Linux. Read on for complete details about the new installer as well as information on how to switch on our new, faster shell environment, the latest webinar news, Jason McLellan's member tale, a software release with twelve updates and six new applications, four new members to welcome, SBGrid citations from four member labs, and three member publication highlights.
We are excited to roll out our new software installer for all SBGrid member labs. This tool is designed to allow individual users to install, update, and manage as many or as few of the software titles in our collection as desired on a desktop or laptop. The installer provides a graphical user-interface for Mac users and a command line interface is also available for both Mac and Linux machines. We think users will find this new tool invaluable, allowing easier access to software on an individual user basis. Please email email@example.com to start the registration process.
Did you know that SBGrid has a new shell environment that loads almost instantly and is faster to run? It also makes managing duplicate executables between applications easy. Try it out with the 'sbcap on' command. You can switch back to the old environment with the 'sbcap off' command. Find out more info on our wiki https://sbgrid.org/wiki/capsules and email us at firstname.lastname@example.org if you encounter any problems.
Be sure to join our Tuesday webinar tomorrow, when Willy Wriggers will give a follow-up presentation, this time on his application Sculptor, an interactive graphics program for multi-scale modeling of density maps and atomic structures. If you missed Dr. Wrigger's SITUS webinar last month, you can catch it on the SBGrid YouTube channel.
Jason McLellan at the Geisel School of Medicine, Dartmouth College is the focus of our October member tale. McLellan talked to us about his work on fusion proteins in viruses like HIV and RSV, and how structure-based vaccine design nicely marries the basic science that he is doing in structural biology to understand how proteins function with his translational work using this structural information to design antigens that intervene before viruses cause infection. Read the full story.
We pushed out a big software release in October, including updates to BioXTAS RAW, Bsoft, CCP4, CTFFIND4, DIALS, HKL2000, Phenix, PyMOL, Rosetta, Scatter, Simulaid, and XDS, along with 6 new software titles: Globus Connect Personal, Gwyddion, MotionCor2, RSF, ShapeMapper, and SuperFold.
Four new members joined SBGrid during the month of October: Janet Smith, Jeanne Stuckey, and John Tesmer from the University of Michigan and John Tainer from MD Anderson. 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 in member publications during the last month. We got a nod from Catherine Drennan's group at MIT in the Journal of Biological Chemistry [PDF], in a new Nature paper from Ryan Hibbs's group at UT Southwestern [abstract], in a new bioRxiv [preprint] from Cameron Mura's group at the University of Virginia, and from Dirk Niessing at the Institute of Structural Biology, in a paper appearing in Acta Crystallogr F Struct Biol Commun [PDF].
Over 46 publications from SBGrid member laboratories have appeared in journals since our last newsletter. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Axel Brunger's group at Stanford continue their work on data processing with X-ray free electron laser technology and describe in their eLife paper improved methods used for reprocessing the synaptotagmin-1 / SNARE complex. [PDF]
- In a new Nature Communications article, Andrés Palencia, from the University Grenoble Alpes, describes how antibiotic-producing microbes have developed structural changes in tRNA-dependence that help therm resist their own toxins. [abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues highlights a Nature paper, to which Barry Honig's group at Columbia contributed, that reveals how the cancer-fighting molecule p53 is reactivated when the SET protein is repressed. [More on Tumblr].
BioXTAS RAW version 1.2.0 is now available. Since our last update the developers pushed out big changes in version 1.1.0, which represented a major milestone with the full integration of the RAW code along with new solid angle correction for integrating images into scattering profiles, improved speed (up to a factor of 7 faster) when calculating Rg, MW, and I(0) for SEC-SAXS curves, and the ability to read in multi-wire (.mpa) files and headers from the SAXS beamline BL19U2 at the Shanghai Synchrotron Radiation Facility, Version 1.2.0 adds two major new features: the ability to perform SVD on a set of scattering profiles, IFTs, or a SEC-SAXS curve, and implementation of the evolving factor analysis (EFA) method for deconvolving overlapping data. The developers note that while EFA is an exciting new technique, they are actively developing this tool for improved stability and utility of the algorithm.
Bsoft was updated to version 1.9.2.
CCP4 is now at version 7.021.
CTFFIND4 version 4.1.5 was pushed out. This version is faster than 4.0, includes an option to fix the amount and angle of astigmatism, a warning if CTF aliasing is detected, has improved diagnostic 1D plats, and resamples data when the input pixel size is too small (switch off using expert options).
DIALS was bumped to version 1.3.5. Changes since our last update include improved support for processing compressed images, more efficient parallel processing in dials.find_spots, improved responsiveness to parameter changes in dials.image_viewer, the ability to display resolution ellipses when the detector is at 2theta angle > 0, and updates to the distl spotfinding webserver: new versions of apache and mod_python and expanded support for the dials spotfinder, including native support for Eiger HDF5 data from Dectris.
Globus Connect Personal version 2.3.3 (Linux) and 2.3.5 (Mac) was added to the SBGrid collection. This tool creates a Globus endpoint on your laptop or other personal computer and allows you to transfer and share files, regardless of whether you have administrative privileges on your machine.
Gwyddion is new to SBGrid. Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis at version 2.46.
With HKL2000 version 714 users have a new optional version of the frame display program XDisp Qt. To activate this new version, select 'Options --> Xdisp --> XDisp Qt'. The selection can be saved for the next sessions using 'Options --> Save options'.
MotionCor2 version 08/22/2016 is another new addition. MotionCor2 is an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.
The Phenix nightly build 1.11-2567 is now available.
PyMOL version 22.214.171.124 was pushed out. This version includes support for several new file formats and a new "unset_deep" command that clears settings on all levels,
RELION has been updated to include an add-on called 1.4-randomphase3d. This little jiffy allows RELION to do random phase 3D classification. To access this tool users will need to select RELION version 1.4-randomphase3d as a version override in their ~/.sbgrid.conf file.
Rosetta version 3.6 was pushed out. This update includes new scorefunctions along with many other new tools, applications, and features. We also made an old version of Rosetta available per a user request (version 2.3.1), which includes a multi-graft tool that is not available in newer versions.
RSF, or the RNA Structure Frameworks, is a modular toolkit developed to deal with RNA structure probing high-throughput data, from reads mapping to structure deconvolution. Read more on the RSF website.
Scatter is now at version 3.0h. Since version 3.0 you may notice several updates to the Subtract tab, including a new Save feature, an option to calculate the Signal Plot using Subtracted Data (just add the subtracted set into the Samples List and hit Signal Plot), and an option to exclude points in Auto-Rg to reduce noise near beamstop. Also new is an SVD button in the Analysis and Subtraction tab and critical updates to inverse Fourier transform.
ShapeMapper version 1.2 is new to SBGrid from Kevin Weeks's lab. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides extensive diagnostic information useful for experiment analysis and troubleshooting.
Simulaid was updated to version 20161012
SuperFold is another new title from the Weeks Lab. At version 1.0.0, SuperFold is a pipeline that uses data obtained from ShapeMapper to model RNA secondary structures, including pseudoknots, identify de novo regions with well-defined and stable structures, and visualize most probable and alternative helices.
XDS is now at version 20160617, which includes improvements to image cache efficiency and squashes a bug that appeared in May 2016 in XDSCONV when converting XDS files to filetype CCP4 using GENERATE_FRACTION_OF_TEST_REFLECTIONS.
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.