SBGrid Consortium - News and Events

Newsletter for October 2022

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Published October 2022

Dear Consortium Members and Affiliates,

October news from the SBGrid Team includes a TomoTwin-cryoet webinar on Nov 8th, a software push with 8 updates and 4 new titles, 2 new members to welcome, some technical notes on the new MacOS, new size recommendations for the full SBGrid software collection, and RELION release notes, and 3 member publication highlights.

Next up for our software webinar series, join us on November 8th to hear from Thorsten Wagner on a brand new tool: TomoTwin-cryoet, for particle picking in Tomograms using triplet networks and metric learning. Register here for the series. Many thanks to Jan Koskinski for kicking off the series in October with a primer on Assembline. The video for that talk will be up on the SBGrid YouTube channel by the end of the week.

Upcoming SBGrid Webinars

Nov 8: Thorsten Wagner - TomoTwin-cryoet

Dec 13: Thomas Simonson - Proteus

Jan 10: TITAN: Getting the most from NMR titration experiments with two-dimensional lineshape analysis

Feb 14, SPECIAL TIME - 10am EST: Martin Steinegger - Fast and accurate protein structure search with Foldseek

Mar 14: Kiarash Jamali, Scheres Laboratory - ModelAngelo: Automated atomic model building for cryo-EM

Apr 11: Gustaf Ahdritz - OpenFold

May 9: to be announced

Jun 13: Woonghee Lee - POKY

Webinar registration and details here

Our October software push includes updates to Aretomo, Avogadro, CCP4, COOT, ISOLDE, RELION, SCIPION, and Xmipp, along with four new titles: IDPConformerGenerator, model-angelo, Paramagpy, and the topaz-filament fork. See Software Changes below for complete details.

Two new members joined in the month of October: Andrew Ellington from University of Texas at Austin and Aaron Whitely from University of Colorado, Boulder. Welcome to our newest members!

Technical Notes from the Software Team

New Mac OS release: MacOS 13 Ventura was released this week, adding new functionality and dropping support for a number of mac computers. As with all new OS releases, we advise against major OS updates on your production workstations until we can complete application testing.

Increased size recommendation for site installations: The number and size of scientific software titles has expanded dramatically over the last year. We want to keep adding the latest versions of titles like Alphafold and RELION while also providing versioning, continuity, and support for multiple architectures. We also want to include larger titles, machine learning models, and structure libraries when possible. To this end, we are now recommending 2T of disk space to store all versions of all software titles for both macOS and Linux and leave sufficient space for future growth. If you manage a site installation and 2T is too much, we can make site-specific adjustments to accommodate your configuration. Contact us at bugs@sbgrid.org for more information.

Attention RELION users -- versions 4.0.0 and 3.1.4 are officially released! The Scheres group released official versions of the 4.0 and 3.1 series of RELION. These latest releases incorporate many bug fixes and both are available for Linux and macOS. If you are using older “beta” RELION releases, please update to the latest version or let us know at bugs@sbgrid.org. We will soon remove the many “beta” versions of the software from the SBGrid collection.

Member Publications Highlights

Over 50 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:

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In a new paper in Analytical Biochemistry, Rick Page of Miami University in Ohio devised a fluorescence dequenching-based assay for tobacco etch virus (TEV) protease to quickly quantify TEV protease activity and mitigate the poor activity associated with inadequate TEV protease preparation. [Abstract]

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A fun In Your Element piece in Nature Chemistry from the University of Michigan's Jennifer Bridwell-Rabb takes us on a journey into the history of chlorophyll, dubbed the green pigment of life, and its functions. The paper includes a timely reference to the modern quest for sustainable clean energy as well as a playful allusion to the Marvel Series. [Abstract]

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From our graduate student desk, Harvard student Kristen Rodrigues highlighted a publication from the laboratory of Markus Seeger at the University of Zurich in which the authors describe their use of a spin-labeled nanobody to study the structural states of MsbA through double electron-electron resonance in E. coli cells and the unexpected prominence of inward-open conformation, typically viewed as irrelevant. [Read more].

Deposit your experimental datasets: If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.

Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.

Please use this SBGrid logo on the acknowledgements slide of your presentations.

We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software:

Structural biology applications used in this project were compiled and configured by SBGrid [1].

[1] 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 citations: SBGrid's eLife paper received 7 new citations in the month of October, from these SBGrid-member laboratories:

Alan Brown of Harvard Medical School in PNAS: SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules; Stephen Burley of Rutgers in Biomolecules: Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Student; Rachelle Gaudet of Harvard University in Nature Chemical Biology: Structural basis of colibactin activation by the ClbP peptidase and A small molecule inhibitor prevents gut bacterial genotoxin production; Marc Kvansakul of La Trobe University in Viruses: Crystal Structures of Epstein–Barr Virus Bcl-2 Homolog BHRF1 Bound to Bid and Puma BH3 Motif Peptides; Roderick MacKinnon of Rockefeller University in Neuron: Structural and functional analyses of a GPCR-inhibited ion channel TRPM3; Guy Schoehn of Institut de Biologie Structurale (IBS) in Viruses: The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction; Niraj Tolia of National Institute of Allergy and Infectious Diseases in Nature Communications: Neutralizing and interfering human antibodies define the structural and mechanistic basis for antigenic diversion.

Software Changes

AreTomo was updated to version 1.3

Avogadro was updated to release 1.2.0 for the default, and 1.9.7 is available via version override as the latest Beta for Avogadro 2.0.

CCP4 8.0.005 is now available via version override.

COOT was bumped a couple of releases to 0.9.8.5 and includes updates to include the AlphaFold pLDDT colour scheme, ignore carbonyl oxygens in merge fragments, allow refinement of inter-chain links, and re-enable the picking of hydrogen atoms in rotation/translation.

IDPConformerGenerator 0.6.15 is new to SBGrid. IDPConformerGenerator is a modular platform for generating ensembles of disordered protein states that builds conformers by sampling backbone torsion angles of relevant sequence fragments extracted from protein structures in the RCSB Protein Data Bank.

ISOLDE 1.4 was updated for compatibility with ChimeraX 1.4. The GUI was completely revamped and rebuilt for more consistency and usability. The most-used controls are now in the top ChimeraX ribbon menu.

ModelAngelo is new to SBGrid at version 0.0.1. The latest tool from the laboratory of Sjors Scheres, ModelAngelo is an automatic atomic model building program for cryo-EM maps. It works best when users have access to GPUs with at least 8GB of memory. Mark your calendar for March 14th, when Kiarash Jamali introduce ModelAngelo as part of our webinar series.

Paramagpy 1.2 is also new. Paramagpy is a python module for calculating paramagnetic effects in NMR spectra of proteins and includes fitting of paramagnetic susceptibility tensors to experimental data associated with pseudocontact shifts (PCS) residual dipolar couplings (RDC), paramagnetic relaxation enhancements (PRE) and cross-correlated relaxation (CCR). It also has a GUI for easy viewing of data and a seamless transition between PCS/RDC/PRE/CCR calculations.

RELION 4.0 is out, with a new approach to subtomogram averaging with better weighting of the individual 2D images that make up a tilt series in relion_refine implementation of single-particle concepts of Bayesian polishing and CTF refinement for tomography data. Also new is a Variable-metric Gradient Descent with Adaptive Moments (VDAM) refinement algorithm for faster 2D and 3D classification, automated 2D class selection, a framework for automated execution of predefined workflows, and tighter integration of the pipeliner with CCP-EM software

SCIPION release 3.0.12 is out and available via version override. Note: due to its large size this software is available for inclusion by request.

topaz-filament 20220325 is a new fork of Topaz for helical filament picking.

Xmipp was updated to 3.22.07.

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.

This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.

More information about the SBGrid Consortium is available at https://sbgrid.org

Report software bugs: sbgrid.org/bugs

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