Dear Consortium Members and Affiliates,
In our last update before things ramp up for the academic year, we have a September webinar reminder, new jobs postings from several member labs, a software push with 13 updates, five new members to welcome, and thee member publication highlights.
Next on the webinar front: an update from SBGrid's Jason Key on the new SBGrid environment and installation tools. Join us on September 19th at 12:00pm to hear more about what's new and where things are going at SBGrid. Details here.
Several of our member labs have open positions posted on our website. Check out postings from the laboratories of Leemor Joshua-Tor at Cold Spring Harbor Laboratories, Anna Pyle at Yale University, Celia Schiffer at UMass Medical, and Walter Chazin at Vanderbilt University. More details for each on our Job Postings Page.
We pushed out a bevy of software updates this month, with new versions for: ATSAS, Bsoft, CARA, CCP4, Coot, MDAnalysis, MotionCor2, NMRpipe, Phenix, PowerFit, RELION, Scipion, and xdsme.
August also brought us five new members, including Michael Cianfrocco from the University of Michigan, Peng Yuan from Washington U St. Louis, and three new faces from UT Southwestern: Xiaochun Li, James Chen, and Diana Tomchick. 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 2 new citations in the month of August, one from from John Kuriyan at UC Berkeley in eLife [Abstract] and a second from Jason McLellan at Dartmouth School of Medicine in PNAS. [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:
- A publication from Alexandre Bonvin's Utrecht University laboratory, appearing in Scientific Reports, describes a new tool for predicting hot spots on protein interfaces - the SpotOn web server. [Abstract]
- In a new Science publication from Karolin Luger's laboratory at the University of Colorado, Boulder reveals similarities between archaeal DNA folding and the eukaryotic nucleosome, supporting an ancestral link. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a publication in Nature Communications co-authored by SBGrid member Guy Schoehn from IBS Grenoble, which unravels some of the mystery behind the efficiency of phytoplankton photosynthesis [More on Tumblr].
ATSAS version 2.8.2-2 now supports Ubuntu 16 and Debian 8 and includes a number of new tools: secplot, a point-and-click interface to process SEC-SAXS data; sasres, to estimate resolution of ab initio shape reconstruction; parcoor, to partition protein coordinates (PDB) into subdomains according to dynamics (NMA); seqstat, to get statistics about a protein from its amino acid sequence; pdbstat - for protein statistics in a PDB file; databsolute, to normalize a SAXS curve to an absolute intensity scale; and adderrors, a simple tool to add simulated experimental errors to a dataset.
Bsoft version 1.9.5 includes lots of bug fixes and improvements.
CARA version 18.104.22.168 is a beta release that includes many behind the scenes changes that will make it easier to develop CARA, including a completely new scope for 4D spectra (FourDScope) analysis. The Qt/Lua binding has been completely rewritten and Lua script writing is easier, with a full-featured debugger in CARA Explorer. The SBGrid default is still the last stable release (CARA 1.9.0), but this beta version is available via a version override.
CCP4 version 7.0.043 was pushed out.
COOT 0.8.9-pre-revision-6870 is another pre-release version that is available as a version override for those who want to try out the latest updates.
MDAnalysis version 0.16 includes many bug fixes and enhancements.
MotionCor2 version 1.0.0 has several new features including batch processing of TIFF movies, correction of fixed-patterns of camera defects, archiving movies stacks in 4-bit format, anisotropic mag correction, and options to run on various GPU architecture from sm_30 to sm_61.
NMRpipe is now at version 20170620.
Phenix version 1.12-2829 includes four new tools: phenix.secondary_structure_validation, Structure Comparison, phenix.mtriage, and phenix.real_space_diff_map. Many other improvements: better sharpening algorithms in phenix.auto_sharpen; better iterative map improvement in phenix.map_to_model; individual mapping in phenix.map_to_object; better outlier rejection in ssm-rmsd calculation in phenix.find_alt_orig_sym_mate; and new GUI interfaces for phenix.mtriage, phenix.map_box, phenix.auto_sharpen, phenix.map_to_model, phenix.ncs_average, and phenix.sculpt_ensemble.
PowerFit is now at version 2.0.0
RELION version 20170802 is the new default. This version includes Implementation of the Stochastic Gradient Descent algorithm for initial 3D model generation, and functionality to impose helical symmetry in sub-tomogram averaging and impose local symmetry, much like non-crystallographic symmetry in X-ray crystallography. RELION was also patched following an adviosry from the developers.
SCIPION 1.1 was also pushed out. This version includes improvements to EM package integration: an update for Relion 2.0.4 and additions for Motioncor2, gCTF, and gAutomatch. The single movie alignment protocol was split into several, with one for each program, and as always there was much focus on usability improvements and bug fixes. Scipion now works in “streaming mode”, allowing users to compute aligned movies and estimate CTF as soon as a movie or micrograph comes out of the microscope PC.
XDS version 20170720 brings back parallel processing, in case data processing overlaps with the measurements, and the parameter value maxcpu in the shell script forkxdsto, to simplify installation of XDS on a supercomputer cluster using a SLURM workload manager.
XDSme was updated to the latest version 20170725.
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.