SBGrid Newsletter: November 2025

Dear Consortium Members and Affiliates,

We're sending our November news along with December greetings, as the SBGrid team returns from the Thanksgiving Holiday. Read on for a story featuring Prof. Melanie Ohi, a link to our most recent webinar, a software push with ten updates and five new titles, and one member publication highlight.

Thinking about upgrading your MacOS to Tahoe? Wait! Learn more in the technical notes from our software team below.

Melanie Ohi is the focus of our November member tale, who you may find outside her University of Michigan laboratory cycling the gravel paths around Ann Arbor. Ohi stuck with cryoEM, despite warnings that becoming a "blobologist" would limit her options, and is excited by the immediacy and the range of resolutions that cryoEM offers in her study of membrane proteins. [Read the full story] 

For our November software webinar we heard from Hui Wang from UCLA on TomoNet - Automatic Particle Picking of Flexible Lattice-Like Structures for CryoET. If you missed it, you can watch the recording on the SBGrid YouTube channel. We'll take a break in December, but mark your calendars for January 13th when our own Alice-Roza Eruera will give a primer on Building CryoET Training Workflows Using the SBGrid Ecosystem. 

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

January 13:  Alice-Roza Eruera - Building CryoET Training Workflows Using the SBGrid Ecosystem

February 10: Open Free Energy

March 10:  Open Force Field

April 14: Jose Luis Vilas - Image processing made it simple with scipionTomo

May 12: Jarrett Johnson - PyMOL

June 9: Mart Last -  Ais and Pom

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 BCFTools, BioXTAS RAW 2, CCPEM-Pipeliner, CNIO relion_tools, COOT, Doppio,  OpenEye, RDKit,  Scipion, and Surface-morphometrics, along with five new titles: CryoAtom, CryoCAT, CryoLithe,  CryoSiam, and Protein-Hunter. See Software Changes below for complete details.

Two new members joined in the month of November: Wayne Patrick from Victoria University of Wellington and Ceesar Santiago from Centro Nacional de Biotecnologia  in Spain. Welcome to our newest members!

MacOS 26 Tahoe issues: We recommend that users hold off upgrading to MacOS Tahoe since XQuartz-based OpenGL acceleration is partly broken. These issues impact software that rely on XQuartz, such as Coot. 

COOT Update: We have added a stand-alone versions of Coot for Linux and for ARM and Intel-based Macs that are available for academic, non-profit, and commercial members to download. These versions will work with MacOS Tahoe and are not dependent on other applications. Additional details in the Software Changes section below.

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:

- Recent PhD graduate KeAndreya Morrison highlighted a publication from the laboratory of Mihnea Bostina from the University of Otago and colleagues, who uncover the first high-resolution, head-to-tail structural map of a Felixounavirus bacteriophage, revealing how these viruses latch onto bacterial cells and offer new clues for designing next-generation antibacterial therapies. [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 seven new citations since our last reporting, from these SBGrid members: 

Demet Araç from the University of Chicago in PNAS: The far extracellular CUB domain of the adhesion GPCR ADGRG6/GPR126 is a key regulator of receptor signaling

Titus Boggon from Yale University in Protein and Peptide Letters: Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

Seth Darst at The Rockefeller University in Nature Communications: Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase 

Jean-Philippe Julien from The Hospital for Sick Children Research Institute in Journal of Virology: Human antibody targeting of coronavirus spike S2 subunit is associated with protection mediated by Fc effector functions, and in JACS Au: Molecular Insights into the Engagement of High-Affinity Sialylated Ligands to Human CD22

Andrew Kruse from Harvard Medical School in PNAS: Conformational regulation of two essential activators of bacterial cell elongation

Ci Ji Lim from University of Wisconsin-Madison in Science: Human RPA is an essential telomerase processivity factor for maintaining telomeres

Rick Page from Miami University Ohio in Biochemical and Biophysical Research Communications: Functional and structural analyses of UbcH5 mutants with enhanced binding to the E3 ubiquitin ligase CHIP

Andres Palencia from University Grenoble Alps in Nature Communications: Hierarchical folding-upon-binding of an intrinsically disordered protein

Susan Shao from Harvard Medical School in Nature Communications: Structures of human organellar SPFH protein complexes

CryoAtom 20251117 is a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information. It uses a two-stage approach: first predicting C-alpha atom coordinates from the density map, then building the full-atom model by combining sequence and density information. The tool can work with or without sequence input and includes capabilities for protein refinement, sequence identification from databases, and handling of masked density maps.

https://github.com/YangLab-SDU/CryoAtom

CryoCAT 0.6.1 is a library providing contextual analysis tools for cryo electron tomography and subtomogram averaging.

https://github.com/turonova/cryoCAT/releases 

CryoLithe a37b49e is a supervised machine learning method to directly reconstruct the tomogram from aligned cryo-ET tilt series. The method is trained on real measurements using FBP+cryo-CARE+IsoNet reconstructions as the reference. The network exploits the imaging geometry to extract small patches from the tilt series to recover the volume.

https://github.com/swing-research/CryoLithe?tab=readme-ov-file#updates 

CryoSiam 1f202e0 is a self-supervised deep learning framework that works on dense and subtomogram levels. The dense part of the framework is additionally trained on subtasks for tomogram denoising, semantic segmentation (particle identification), and instance segmentation. The subtomogram level part of the method offers embedding representation of the detected particles in the tomogram/s.

https://github.com/frosinastojanovska/cryosiam 

Protein-Hunter 465c7d2 exploits structure hallucination within diffusion for protein design. A fast, fine-tuning-free framework for de novo protein design. 

https://github.com/yehlincho/Protein-Hunter 

BCFTools 1.22 adds the liftover plugin, which converts genetic variants across genome assemblies.

https://academic.oup.com/bioinformatics/article/40/2/btae038/7585532#438467595

BioXTAS RAW 2.4.0 introduces a new multi-series analysis module that enables profile-by-profile averaging, subtraction, and manipulation across multiple series simultaneously, useful for complex analyses like point-by-point buffer subtraction in IEC-SAXS elutions or time-resolved SAXS data processing. This release also updates DENSS to the latest version and fixes numerous bugs affecting HDF5 file loading, detector integration, molecular weight calculations, and workspace functionality.

https://bioxtas-raw.readthedocs.io/en/latest/changes.html

CCPEM-Pipeliner 1.4.0 is out. There are no release notes available.

https://gitlab.com/ccpem/ccpem-pipeliner/-/tags/v1.4.0

CNIO relion_tools 0df39a2 includes minor changes to the README file to indicate support for Relion 5 and dependency version changes to better support more recent operating systems.

https://github.com/cryoEM-CNIO/CNIO_Relion_Tools

COOT 1.1.19 is now available for Linux and Mac. For ARM and Intel-based Macs, the version appears as 1.1.19_arm and 1.1.19_x86. This version of Coot is the first SBGrid build and does not depend on CCP4. Changes specific to the 1.1.19 release include an option to doubl-click to label symmetry atoms, drag-and-drop import for local-file-system files, the return of the user-defined-clicks function, Assign and Associate Sequence menu item functions added back, and improved scrolling of the map contour level when the nominated map is not displayed.

https://github.com/pemsley/coot/releases/tag/Release-1.1.19

Doppio 1.4.0  adds new features as job continuation and overwriting support, Chimera (.defattr) attribute file support for visualisations, new scripts for automatic ssh port forwarding. It also updates processing of predicted models to AlphaFold fetch job, graphical outputs to Topaz training job, improved B-factor distribution and FSC plots in Validation and Servalcat jobs, updates to LocScale, ModelCraft and em_placement jobs and various minor bug fixes and updates.

https://www.ccpem.ac.uk/docs/doppio/release_notes.html 

OpenEye 2025.1.1 adds OpenEye viewer (VIDA).

https://www.eyesopen.com/vida 

RDKit 2025.09.2 includes backwards incompatible changes to SMARTS parsing, CIP ranking behavior, and hydrogen removal handling. This release adds performance improvements for MolFromSmiles with chain molecules, enhanced RGroupDecomposition supporting multiple core hits, and new Python wrappers for reaction processing. Notable bug fixes address hydride removal in organometallics, CSharp wrapper Linux builds, and various segmentation faults.

https://github.com/rdkit/rdkit/releases/tag/Release_2025_09_2

Scipion 3.7.1 includes a CryoSPARC plugin to Scipion in SBGrid. Since there is no native CryoSPARC install in SBGrid, to use this plugin in Scipion you will need to link a functional CryoSPARC install to Scipion following these instructions these instructions. Please note that Scipion core has the latest version (scipion-em@3.10.2, scipion-pyworkflow@3.11.2, scipion-app@3.8.3), but we kept the version name “3.7.1” in SBGrid because recent updates were minor.

Surface-morphometrics 1.1 supports updated pymeshlab API and deals with missing pyto dependencies.

https://github.com/GrotjahnLab/surface_morphometrics/releases/tag/1.1 

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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