SBGrid Newsletter: October 2024

Dear Consortium Members and Affiliates,

It's the Halloween evening edition, as October comes to a close. Our news for the month includes a reminder to tune in for  our upcoming webinar on QuaRef, a software push with nine updates and three new titles, a note from our technical team about potential issues with MacOS Sequoia, three new members to welcome, and two member publication highlights.

We kicked off our software webinar  with a presentation on qFIT from Stephanie Wankowicz of Vanderbilt University. You can watch a recording of this webinar on the SBGrid YouTube Channel. Next we'll hear from Pavel Afonine of Berkeley Lab on November 12th with an introduction to QuaRef: Machine Learning Accelerated Quantum Refinement of Protein Structures.

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

Nov 12: AQuaRef: Machine Learning Accelerated Quantum Refinement of Protein Structures - Pavel Afonine

Dec 10:  AreTomo3: Real-time Processing Pipeline for Generating 1,000 Accurate and Contrast-Enhanced Tomograms - Ariana Peck

Jan 14: MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography - Lorenz Lamm 

Feb 11: Phenix/OPLS and GlideEM:  Enabling cryoEM structures for drug discovery with the Schrodinger Suite - João Rodrigues

Mar 11: Structure modeling and Validation using AI-based methods: DeepMainmast and DAQ - Genki Terashi

April 8: Warp - Dimitry Tegunov

May 13: DRGN-AI - Ellen Zhong

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 cryoDRGN, CryoSieve, cyrosparc-tools, DIALS, MemBrain-Seg, PHYLIP, qFit, ShelXle, and Warp, along with three new titles: AMPLIFY, ChemEM, CryoSegNet. See Software Changes below for complete details.

Three new members joined SBGrid in the month of October: Alireza Ghanbarpour of Washington University in St. Louis, Ariane Briegel from Institut Pasteur, and Jungsan Sohn from Johns Hopkins University School of Medicine. Welcome to our newest members!

MacOS Sequoia rsync to opensync issues: With the release of macOS 15 Sequoia, Apple has changed from rsync to openrsync. Openrsync aims for compatibility with modern rsync, but accepts only a subset of rsync's command-line arguments. We have seen problems using this openrsync build with the SBGrid Installation Manager. While configuration changes on the server side have mitigated the impact on users, we will soon release a new version of the installation manager to accommodate the limited rsync functionality. Please let us know if you experience problems with your installation manager on macOS 15. 

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 in Acta Crystallogr F Struct Biol Commun from SBGrid member Graham Chakafana of Hampton University in which the authors use crystallography to better understand a new potential target for anti-malarial drugs. [Read more]

- Meharry Medical College student KeAndreya Morrison's highlight features a publication that appeared in PNAS from the laboratory of Vincent Tagliabracci, of University of Texas Southwestern Medical Center, in which the authors studied RLIG1, a unique enzyme that repairs broken RNA by binding and reconnecting RNA ends, providing insights into how it helps maintain cell function. [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: 

Catherine Drennan of MIT in PNAS: Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy; Ramachandran Murali from Cedars-Sinai Medical Center in Nature Communications: The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2; 

AMPLIFY 20241008 was just added to the SBGrid collection. AMPLIFY is a protein language model that leverages advanced machine learning techniques to analyze and interpret protein sequences that includes functionality for protein property prediction and sequence-to-text comparisons. It also provides robust performance across various protein-related tasks.

ChemEM is new to SBGrid at version 0.0.3. ChemEM is a tool for accurate small molecule docking in cryo-EM maps, utilizing density information and state-of-the-art small molecule force fields to dock ligands into protein targets.

cryoDRGN 3.4.1 is the new default.. This patch release addresses some minor issues and improves compatibility with the default output number format used by the most recent versions of RELION

CryoSegNet 1.0.0 is another new title. CryoSegNet is a cutting-edge software designed to enhance cryo-electron microscopy by using advanced AI techniques for accurate particle detection in cryo-EM images. Trained on a diverse range of protein types, CryoSegNet produces output compatible with popular cryo-EM software. Read the publication for more information.

CryoSieve 1.2.8 is now available. In addition to bug fixes, this release includes an  update to the module cryosieve-csrefine. Multiple repeats will share the same Import Particles job, and several additional arguments are now implemented and allowed, including additional local research.

cyrosparc-tools version 4.6.0  introduces new dataset methods, memory-efficient loading, and additional asset support for improved cryo-EM data processing workflows.

DIALS 3.21.1 fixes Xia2 compatibility with XDS 20240723, which changed some output in INTEGRATE.LP. New features include added classes to support time-of-flight and Laue indexing and refinement and support for exporting still data in mmcif format that GEMMI can read. 

MemBrain-Seg version 0.0.2 includes a number of fixes and improvements.

Phenix 1.21.2 is a bug fix release that corrects several issues, including issues where X-ray data parameters (e.g. resolution) are not used, non-default map coefficient parameters cause map names to be numbered, and where the phenix.refine parameter diff could not be saved. For a complete list of changes, see the CHANGES file in the Phenix installation. 

PHYLIP is now at version 3.698, which was released under an open source license. This release also fixes a consensus tree bug.

qFit was updated to version 2024.3. This update introduces improvements to ligand multiconformer modeling, protein modeling capabilities, and includes various code optimizations and bug fixes for improved performance and compatibility.

ShelXle 1.0.1678 includes various developer bugfixes and is newly ported to QT 6.

Warp 2.0.0dev29, the latest developer release, is now available. 

XDS 20240630 re-release and 20241002 are now available. Version 20241002  addresses changes made in the previous release that led to unexpected behavior with certain datasets. Compared to the July release, 20241002 differs in the use of the background template, which is done more subtly by local fitting. It gives more accurate results, but may use more computing time. The re-release of version 202406030 will allow Linux users to revert to the previous version if desired (no similar MacOS version is available). For complete changes, see 

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.

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

Report software bugs: sbgrid.org/bugs