As the winds of May rush past, welladay, we begin a headlong push toward summer, and have a month of SBGrid news to share, including updates to our administrative infrastructure, a webinar to add to your calendar and one to watch online, a new SBGrid tale, a software push with two new titles and 19 updates, four new members to welcome, and 3 member publication highlights.
We're in the midst of several updates to our administrative infrastructure, with this newsletter the first to go out from the new system, hopefully finding its way to your inbox (and not your spam folder). This change is the first of several from what will become a more flexible and efficient system for communication. Please contact us if you notice any problems along the way.
Our May webinar, featuring Thorsten Wagner of the Max Planck Institute of Molecular Physiology is now online. Visit the SBGrid YouTube channel to learn about "Fast, accurate and easy particle picking with crYOLO." Next up we'll here from Colin Palmer from the Science & Technology Facilities Council on Model Building and Validation in CCP-EM. Mark your calendar and join us on July 23. [Read the full story.
This month's software push includes two new applications - emClarity and MoRDa - and 19 updates: BioXTAS RAW, Clustal Omega, crYOLO, CrystFEL, CCP-EM, DIALS, DENSS, DSSR, EMAN2, Ilastik, MotionCor2, Phenix1, T-Coffee, PyEM, RELION, ScÅtter, Situs, TomoAlign, and XDSME. See Software Changes below for complete details.
Four new members joined during the month of May: Peter Walter joins a large group of PIs from University of California, San Francisco, Marc Therrien becomes our second member at the University of Montreal, Jeremy Nathans our fourth at Johns Hopkins, and Ignacio Mir-Sanchis is our first member at Umeå University in Sweden. Welcome to our newest members!
Over 50 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple notable highlights below:
- In Nature's Scientific Reports, Vinit Mahajan's group, at the Stanford School of Medicine, endeavors to improve our understanding of the molecular mechanisms underlying the rare intraocular disease, CAPN5-NIV. [Abstract]
- From the lab of Katya Heldwein at Tufts University School of Medicine comes the cleverly titled publication "Go go gadget glycoprotein!," featured as a "Pearl" in the current issue of PLoS Pathogens and focusing on the diverse modes of viral HSV-1 entry. [Abstract]
- From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication from the laboratories of Eva Nogales and James Fraser at the University of California Berkley and San Francisco. Using high-resolution cryo-electron microscopy and molecular dynamics simulations to study acetylated and deacetylated microtubules, the authors found that K40 in α-tubulin reduced the range of motion and conformational states of the corresponding αK40 loop in which the post-translational modification occurs. [Read more].
- Diana Tomchik of University of Texas Southwestern Medical Center in PLOS ONE: High-resolution cryo-EM structures of the E. coli hemolysin ClyA oligomers. [Absract]
- Frank Sicheri of University of Toronto in Structure: FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane [Abstract]
- Jason McLellan of the University of Texas at Austin in Nature Communications: Transient opening of trimeric prefusion RSV F proteins. [Abstract]
- Pedro José Barbosa Pereiraa of Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal in two publications: International Union of Crystallography: The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation [Abstract] and Journal of Biological Chemistry: The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation. [Abstract]
- Stephen Blacklow of Harvard Medical School in bioRxiv: Molecular basis for feedback inhibition of Notch signaling by the Notch regulated ankyrin repeat protein NRARP. [Abstract]
- Christopher Garcia of Stanford University School of Medicine in Science: Topological control of cytokine receptor signaling induces differential effects in hematopoiesis. [Abstract]
If you're currently preparing a manuscript, please remember you can preserve your primary experimental datasets that support scientific publications. Publish your datasets in the SBGrid Data Bank along with your PDB record deposit and publication submission. We also recommend the following boilerplate language in all publications that report results obtained with SBGrid supported software:
Structural biology applications used in this project were compiled and configured by SBGrid .
 A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
Link to article: https://elifesciences.org/articles/01456.
SBGrid's eLife paper received seven new citations in the month of May, from these SBGrid-member labs:
3dna is now at version 2.4 1. With this update, in x3dna_ensemble the developers have renamed block_image () to blocview and revised its interface of command-line options consistent with other sub-commands. Other changes include a revision to names of atoms and residues in fiber models, a simplified note of ‘simple’ parameters in the analyze program output, and a bug fix for the analyze -t option (for torsion angles) that occasionally pops up.
bioXTAS RAW version 1.5.2 is the new default and you'll notice bug fixes to the electron density output from DENSS, to GNOM, including using data with minimal sampling (<100 points). The .app package for Mac was updated to sharpen the display of text and a modification to the way BioCAT header files are read in was introduced, to accommodate a new header file format at that beamline.
Clustal Omega was bumped to version 1.2.4 to make code gcc-6 compliant.
crYOLO was bumped a couple of releases to 1.3.5. You'll notice increased speed with prediction (30% for picking / 15% for training), after the developers vectorized parts of the code and optimized the creation of the cbox files, along with several other bug fixes.
CrystFEL version 0.8.0 includes support for peakfinder9 and XGANDALF, improved stability to B factors during merging, rejection of patterns during merging according to deltaCCHalf, the introduction of make_pixelmap as a core CrystFEL program, a new command indexamajig --wait-for-file, support for gzipped CBF files, and an update to the build system to CMake from autotools.
CCP-EM version 1.3.0 is now the available and with it comes updates to Relion and Coot (requires version 2.7.11 of XQuartz on Mac OS X), the addition of ProSHADE, for map symmetry determination, map reboxing, etc; SymmetryExpand, which uses Refmac to copy changes from one chain to symmetry-related copies; new results summary graphs and minor pipeline improvements in Buccaneer & Nautilus; in Refmac, a fix to the FSC calculation bug in the half-map validation pipeline along with user interface improvements, plot output improvements in MRC to MTZ, changes to the handling of sharpening/blurring factors for consistency with Refmac and Buccaneer and Nautilus tasks; RIBFIND (FlexEM) improvements to deal with multi-chain PDBs, a renaming of the OpenMPI 'mpirun' wrapper script to 'ccpem-mpirun' to avoids conflicts with other MPI installations; and many other bug fixes.
DIALS was updated to version 1.14.3 (from 1.12.3) and a full listing of changes is available in the release notes.
DENSS version 0190419 is the new default.
DSSR version 1.9.2-2019may06 includes a revised algorithm for the alignment of G-tetrads along a G-helix in addition to other minor code refinements.
EMAN2 was updated to version 2.23
emClarity was added at version 1.0.0. emClarity is a tool for high-resolution cryo-electron tomography and subtomogram averaging, and is new to SBGrid.
ilastik version 1.3.2 was pushed out. With the bump to 1.3.0, ilastik updated all dependencies and switched from Python 2 to Python 3. The developers suggest making copies of all important project files before use with the new version of ilastik because projects created with older ilastik versions may no longer load.
MoRDa version 28 is also new to SBGrid. MoRDa is a pipeline for molecular replacement protein structure solution using X-ray data. The software package includes a database and a set of programs for the structure solution.
MotionCor2 is now at version 1.2.3
Phenix version 1.15.2-3472 includes several improvements to existing tools: a new phenix.map_to_model algorithm for faster and builds longer chains; an updated structural library for phenix.structure_search, an updated ligand library for phenix.ligand_identification, and improved reporting of cis-peptides for residues with altloc atoms. You'll also find several new tools: phenix.trace_and_build for building protein into maps at resolutions as low as 4.5 A; phenix.fix_insertions_deletions to build models in places where the map is poor; phenix.refine_ca_model for optimizing C-alpha only models; phenix.comparama for generating Kleywegt-like plots that show how residues move in the Rakmachandran plots before and after refinement; and eLBOW, to find unique instances of a ligand from the PDB and optionally create Polder OMIT maps
T-Coffee was updated to version 12.00.
PyEM version 0.4 is the new default.
RELION is now at version 3.0.4.
ScÅtter is now at version 3.2b. The jump to 3.2 is a major update with a new FindDmax function to perform a search of d-max and lambda at a fixed q-max, Signal Plot optimization for faster loading, a fix to Chi-square calculation during Pr-refinement tests, a new Pr-function (total diff) for fitting highly asymmetric (long) particles.
Situs version 3.1 was pushed out. This version includes the new DDforge tool for flexible refinement of protein structures against intermediate resolution density maps.
TomoAlign was updated to version 201901.
XDSME version 0.6.6 is now available. This version explicitly invokes python2 to avoid python version conflicts and includes several other fixes and improvements.
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.
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