SBGrid Newsletter: May 2024

Dear Consortium Members and Affiliates,

Updates from the SBGrid team for May include a reminder about our June 11th TomoDRGN webinar, a link to the recording for our May Amber webinar, a software push with 21 updates and four new titles, four new members to welcome, and two publication highlights.

Only two software webinars remaining for this academic season. Join us June 11th at 12pm ET to hear from Prof. Joey Davis of MIT on TomoDRGN, a tool that extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles. We'll then close out the season in July with a presentation on matchmaps from Dennis Brookner.

In case you missed our May webinar with Darrin York on Amber, you can watch the recorded version on the SBGridTV YouTube channel.

To receive email reminders about upcoming webinars, please be sure to register for the series! Registration here: https://sbgrid.org/webinars/#register

Jun 11: TomoDRGN - Joseph Davis

Jul 9: matchmaps - Dennis Brookner

Webinar registration and details

SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College.

This month's software push includes updates to 21 titles including bedtools, cryosparc-tools, cryoDRGN, deepTools, DIALS, EMReady, IMP, IMOD, Jalview, IGV, MemBrain-Seg, MGLTools, PEET, Phenix, POKY, PyMOL, R, RStudio, Relion, Rosetta, and XDSGUI, along with four new titles: Bedtk, LipIDens, Starparser, and Warp.  See Software Changes below for complete details.

Four new members joined in the month of May: Sean Davidson from University of Cincinnati College of Medicine, Christopher Gisriel from University from Wisconsin-Madison, Marc Kirschner of Harvard Medical School, and Jose Antonio Marquez from EMBL Grenoble. Welcome to our newest members!

Over 100 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:

- Fisk University student Vida Storm Robertson highlighted a publication from SBGrid member Tobin Sosnick of The University of Chicago that describes the forces at play when disordered proteins are exposed to varying temperatures and salt conditions. Through clever experimental design, Sosnick and colleagues find that the hydrophobic effect is not the only force acting on these peptides. [Read more]

- Meharry Medical College student KeAndreya Morrison's highlight features a publication from the laboratory of SBGrid member Andrew Kruse at Harvard Medical School that paves the way for more effective treatments for cardiovascular illnesses by engineering synthetic antibodies, called nanobodies, for the angiotensin II type I receptor.  [Read more]

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.

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's eLife paper received two new citations since our last reporting, from these SBGrid members: Yang Gao of Rice University in Journal of Biological Chemistry: Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol η catalyzed DNA synthesis; Rick Page of Miami University, Ohio in Journal of Chemical Information and Modeling: Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase.

Bedtk 0.0.1 is new to SBGrid. Bedtk is a simple toolset for BED files. It is less versatile than bedtools but faster and increases performance for simple operations. 

bedtools 2.31.1 is a minor release that fixes compilation issues that have been encountered on more modern platforms and GCC 13.

cryosparc-tools 4.5.0 is the new default. We pushed out 4.4.1, with a minor error data formatting fix, and 4.5.0, which now works with CryOSPARC 4.5 and includes a new argument for queueing clusters and print methods for inspecting available jobs, updates in the copy and symlink operation and larger shapes for dataset fields, fixes in error reporting and union of datasets, and improved documentation.

cryoDRGN 3.3.0 includes a new tool for interpolating a path in the latent conformation space connecting two points in a direct line. You may also notice improvements to the interfaces and a number of bug fixes.

deepTools version 3.5.5 drops support for python 3.7 and deepblue and includes a number of other minor fixes. 

DIALS 3.19.0 includes new options for using dials when image data is not available and to allow asymmetric unit composition using dials.export, improvements to format reading, and a number of other bug fixes.

EMReady 2.0 now supports map improvements for proteins and nucleic acids and ensures that the pixel size of the output map matches the input map. The algorithm is also more robust for weak density signals.

IMP was upgraded to release 2.20.2, which includes minor changes not expected to impact users. The SBGrid team also added commonly used toolkits (numpy, scipy, sklearn, matplotlib, etc) to python.imp. 

IMOD updates to 4.11.25 (default) and 4.12.60 (via version override) are available and include bug fixes for a crash in Ctfphaseflip, a non-functioning “Use Adjusted Track Com File” button, and a problem when running Splitcorrection. 

Jalview 2.11.3.0 features a new and more powerful command line interface, support for in-depth exploration of predicted alignment error (PAE) matrices from AlphaFold in the context of multiple alignments, AlphaFold’s standard Blue-Orange-Red confidence colourscheme, and a substantial number of minor improvements and bug fixes.

IGV is at version 2.17.4 with bug fixes that address performance issues with BigW files and rendering with BAM and TDF files.

LipIDens is new to SBGrid at version 1.0. LipIDens is a pipeline for simulation-assisted interpretation of lipid or lipid-like densities in e.g. cryo-EM structures of membrane proteins. 

MemBrain-Seg version 0.0.1 is now available and includes UNet, several minor fixes and improvements, improved training documentation, and a restructuring of packages.

MGLTools 1.5.7 is now available with a new autodocktools gui as “adt”, an update from 32 to 64 bit as a default on Macs, and new compatibility with ARM-based Macs when Xquartz is available.

PEET 1.17.0 and 1.18.0a are now available. Version 1.17.0 is the new default stable release with updates for Matlab R0222b and a new usePcaMotiveLists. Version 1.18.0a is a pre-released alpha version available via version override.

Phenix was updated to the latest nightly build.

POKY 20240508 is the developers' “build 11/27/2023o” and is available via version override.

PyMOL 3.0.2 includes minor fixes to Timeline, interpolation bar, sequence viewer, and in some commands, MTZ files are now loaded properly on Windows.

R 4.4.0 fixes a recently identified security issue and includes many new features. 

RStudio 2024.04.1 adds support for R 4.4.0.

Relion 5.0 beta3 is available via version override and adds bug fixes to the beta series. SBGrid provides two CUDA versions: 5.0-beta3_cu12.2 and  5.0-beta3_cu11.8.

Rosetta 3.14 provides support for the Rosetta open repository in addition to many other new features.

Starparser is another new title at version 1.55. Starparser is a python package that supports the parsing of Relion starfiles. 

Warp is new to SBGrid at version 2.0.0. Warp is a set of tools for cryo-EM and cryo-ET data processing including: Warp, M, WarpTools, MTools, MCore, and Noise2Map. This tool is newly available for Linux.

XDSGUI 20231229 is the new default. This release includes a bug fix for XDS.INP and XPARAMS.XDS, and a new option to display CBF files written in PETRA-III.

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

Report software bugs: sbgrid.org/bugs