Dear Consortium Members and Affiliates,
With this March newsletter we say hello to spring...sort of. We're insisting on spring, in fact, despite snow showers two of the past five days. Along with spring we're announcing a new AppCiter tool, EMAN2 and GROMACS webinars, a little history on SBGrid member Georgios Skiniotis, a "Data Processing with WSMR" how-to, a welcome to one new member, a software release with 10 updates and 3 new applications, and highlights from some notable SBGrid member publications.
SBGrid's new AppCiter tool is now available on the SBGrid website, allowing users to quickly generate a citation list for the scientific software used in their research. Please visit the sbgrid.org/software page to try it out. Our database contains over 700 citations for just under 300 software applications that are used by structural biologists. Members can select individual applications and then create RIS or BibTeX files for import into EndNote or other citation management software.
We had a big turnout for Sjors Scheres webinar on Relion last week and hope to get that webinar posted to our YouTube channel soon. April brings Steven Ludtke's webinar -- A quick introduction to EMAN2.1 for CryoEM Single Particle Analysis (April 14th at 12:00pm EDT) -- and in May we'll here from the folks at GROMACS for the latest on this molecular dynamics package.
For our March Tale we talked with Georgios Skiniotis from the University of Michigan Life Sciences Institute where he has set up a cryo-EM suite at the forefront of technology to study GPCR complexes and the molecular factories within microorganisms that make polyketides. The ability to tell a story about macromolecules using pictures, Skiniotis tells us, is what first drew him to cryo-EM.
Jean-Philippe Julien from the Hospital for Sick Kids/University of Toronto is our newest SBGrid member. Welcome!
Software changes for March include updates to BLAST+, CCP4, Chimera, FASTA, Geneious, HKL2000, PDB_REDO, PyMOL, SciPy, and XDS in addition to three new software titles: ALBULA, IHRSR++, and the pysam Python module. Details in the Software Changes section below.
SBGrid member labs published over 68 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 Bill Weis and Axel Brunger’s laboratories at Stanford University there is an eLife publication describing a new data processing system for X-ray free electron lasers datasets. This new system offers the possibility of reducing the number of diffraction images that are typically collected in XFEL experiments.
- James’s Berger Lab, from Johns Hopkins School of Medicine, determined a 3.5 Å crystal structure of the eukaryotic origin recognition complex. The article appears in the March 19th edition of Nature.
- Bob Keenan’s group from the University of Chicago determined the crystal structure of the Get3-TA protein targeting complex. The Get3 cytosolic targeting factor chaperons hydrophobic transmembrane domains of TA. Read about it in Science.
ALBULA is new to the SBGrid collection. ALBULA includes ALBULA VIEWER, which allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup.
BLAST+ was upgraded to version 2.2.30. This version includes tasks for BLASTX and TBLASTN that use longer words, support for composition-based statistics in RPS-BLAST, and eliimnates the FASTA parsing bug.
CCP4 version 6.5.006 is now the default. With this CPP4 release you'll see an update to polarization correction for XDS INTEGRATE with vertical spindle in pointless, a new offline mode for updater, extended support for disaccharides and external validation strings in privateer, and bug fixes in refmac hydrogen generation, Molrep multi-copy search, and in many other places.
Chimera was pushed to version 1.10.1 with updates to CASTp URLs to allow data fetching, improved mda performance when displaying sequences in Multalign Viewer and associating sequences with structures, fixes to R 3 and R 3 2 and H 3 and H 3 2 space groups, and improvements in several other places.
FASTA version 36.3.7a is the new default. This version has alignment sub-scoring scripts that have been extended to allow overlapping domains. This requires a modified annotation format and new annotation scripts are available in the fasta-36.3.7/scripts directory to support this new format.
Geneious version 7.1.7 fixes a bug causing the genbank exporter to crash on documents with polymorphism annotations.
HKL2000 is now at the latest version: 706e. With this version support was added for the ADSC PAD HF-4M formats and the find beam position window was improved. Mac users may need to install the latest version of Xquartz from http://xquartz.macosforge.org. Note: this application is only available to sites with a valid license.
IHRSR++ version 1.5 was added to the software tree. This software is a user-friendly extension to Ed Egelman's Iterative Helical Real Space Reconstruction (IHRSR) software. It includes all of the original IHRSR functionality plus the capabilities to determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data.
PDB_REDO was updated to version 6.0 and now includes parallelization (much faster jobs), support for external restraints, improved handling of carbohydrates and LINKs, nucleic acid-specific restraints, more flexible command-line options, and improved validation.
PyMOL version 22.214.171.124 fixes the wall-eye stereo bug.
We added the pysam module (version 0.7.8 Linux/0.8.1 Mac) to our default Python installation. pysam makes it easy to read and manipulate mapped short read sequence data stored in SAM/BAM files. It is a lightweight wrapper of the htslib C-API.
SciPy, another Python module, was upgraded to version 0.15 and includes a new linear programming interface, differential evolution, a global optimizer, and improvements to several other functions.
XDS version 20150301 includes XSCALE improvements for efficient scaling of a large number of data sets, a simple UI to control refinement of segment orientation and translation for a multi-segment detector, and a new utility -- PIX2LAB -- that helps find laboratory coordinates for a user-specified pixel according to a given input file XDS.INP.
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.