Dear Consortium Members and Affiliates,
As we finish our march toward May we have the latest SBGrid news and updates to pass along to you. Read on for a story on SBGrid member Jacqueline Cherfils, details on our PLUMED webinar, a reminder to deposit your x-ray diffraction datasets in the SBGrid Data Bank, our latest software release, details on the June CCP4/APS School, two new members to welcome, and three member publication highlights.
Jacqueline Cherfils, CNRS research director at École normale supérieure (ENS) Paris-Saclay, is the focus of our April member tale. Cherfils got her start in mathematics and game theory, but developed an interest in protein structures while writing code for early graphic modeling software. Small GTPases first caught her eye in the early 1990s, and she has concentrated her efforts on understanding molecular reactions of the Arf, Rab and Rho families ever since. Read the full story.
Be sure to tune in for our webinar on May 22nd at 12pm, to hear from Giovanni Bussa and Massimiliano Bonomi on "analyzing and enhancing molecular dynamics simulations with PLUMED." Webinar details here. And don't despair if you missed April's webinar from Woonghee Lee on NMRFAM-Sparky. You can watch his tutorial and over 100 other webinars on SBGridTV.
The SBGrid Data Bank now has over 400 published data sets from more than 75 different laboratories. Browse the collection of public datasets and learn how you can preserve your own x-ray diffraction data. For those datasets are not yet ready for the public eye, we can accept the deposit and put them hold for release on a future date.
This month's software release includes updates to breseq, CCP4, IMOD, PLUMED, REFMAC, ROSETTA, SCIPION, SPHIRE, and XDS.
The CCP4/APS School in Macromolecular Crystallography - June 18-25 - will offer advanced training for researchers with some expertise in crystallography and experience with CCP4. The School includes lectures by software developers, data collection with samples provided by participants, and computing tutorials led by the lecturers. Lean more at http://www.ccp4.ac.uk/schools/APS-2018/index.php
April brought us two new members: Anthony Fitzpatrick from Columbia University and John York from Vanderbilt. 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 SBGrid Data Bank 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's eLife paper got 2 new citations in April, with a mention from Jean-Philippe Julien from University of Toronto in his new article in the Journal of Virology [Abstract], and from Harvard Medical School's Andrew Kruse in his Nature publication [Abstract].
More than 40 member publications appeared in March journals. You can find a complete listing on our website, along with a few notable highlights below:
- EMBL Heidelberg's Orsolya Barabas has a new paper in a Nucleic Acids Research, where the researchers have determined the pre-integration structure of the transposon IS608 target recognition complex from Helicobacter pylori, the bacteria known to cause ulcers and stomach cancer in primates. Building upon their finding, they've engineered transposon variants of this bacterial insertion sequence that successfully recognize new directed targets, offering the potential for new genetic and treatment applications. [Abstract].
- In Journal of Biological Chemistry, a new publication from Brandt Eichman of Vanderbilt University focuses on clarifying the pathway by which the helicase-like transcription factor (HLTF) directs stalled replication fork regression. The investigators reinforce and expand upon the requisite role of the HIRAN domain in fork remodeling, thus facilitating a greater understanding of the DNA damage response process. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues highlighted a new publication from Peter Sorger's Harvard Medical School laboratory that appeared in Nature Communications and examines the connection between molecular states induced by drugs and cell phenotypes [More on Tumblr].
breseq was updated to version 0.32.0. See the changelog for full details.
CCP4 version 7.0.053 was added
IMOD version 4.9.7 is primarily a bug fix release.
PLUMED version 2.4.1 includes many new modules and actions, which are described in the changelog. Note that users working in version 2.3 should look at the section "Changes leading to incompatible behavior" for possible adjustments to their input files.
REFMAC is now at version 5.8.0091
ROSETTA version 3.9 includes a bevy of improvements with changes to Scorefunction and the API, updates to several applications and RosettaScripts tools, and bug fixes all around.
SCIPION has moved from 1.2beta to a stable 1.2 release that is the new default, with improved Streaming functionality to work better in facilities, updated EM package, and many other bug fixes and enhancements.
SPHIRE version 1 is now available. This version includes SORT3D, a novel 3D sorting program based on concepts of reproducibility that provides insight into data heterogeneity; MERIDIEN for rapid ML 3D refinement, is initiated directly from 3D orientation parameters which allows the user to rapidly perform local refinements of data subsets obtained with SORT3D. Also included in this release is a streamlined process workflow, an improved GUI, and extensive documentation, including tutorials explaining the underlying concepts.
XDS is now at version 20180409. New features since our last update include a new input parameter MERGE_TREE=, effective in the IDXREF step for unknown crystals, that allows the user to select translated reciprocal lattices for merge with the dominant one. XSCALE also now accepts the new input parameter PRINT_CORRELATIONS=, which can be used to prevent printing long lists of pair correlation factors between the scaled data sets. The estimate for the default value for the raster step size in the 3D-histogram used for locating difference vector clusters in the IDXREF step (input parameter RGRID=) was also improved.
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.