SBGrid Newsletter: May 2025

Dear Consortium Members and Affiliates,

With May comes commencement season, and we applaud the students from around the world who graduated this week, and who in turn applauded Harvard President Alan Garber. The SBGrid team continues at full speed during the summer season, and in this May update we have a new profile on George Phillips from Rice University, a reminder about our final webinar for the season, a software push that includes eleven updates and eleven new titles, five new members to welcome, an announcement from NE-CAT about their Data Collection and Processing Bootcamp, and two member publication highlights. 

For our May member tale we met up with George Phillips from Rice University, who looks back on the many phases of his career and ahead to the space that his second retirement will bring to tinker, around the holistic garden at Rice and with new computational approaches to solve the "phase problem" in crystallography. Read More: https://sbgrid.org/members/tale/the_final_phase

In software webinar news, Genki Terashi from Purdue University will join us June 10th to give a primer on DiffModeler & CryREAD. If you missed last week's webinar with Ellen Zhong from Princeton University on CryoDRGN-AI, you can catch the recorded version on YouTube: https://www.youtube.com/watch?v=P9c1dUO3-Hg

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

June 10:  Genki Terashi - DiffModeler & CryoREAD: Macromolecular and Nucleic Acid Structure Modeling for Cryo-EM Maps Using Deep Learning

Looking ahead to the next academic season, please email Michelle if you'd like to suggest a topic for a future webinar.

Webinar registration and details

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

This month's software push includes updates to Boltz-1, CNS, cryoDRGN, MemBrain-Seg, ModelAngelo, PyEM, Relion, Scipion, Topaz, XDS, and Xmipp, along with eleven new software titles: BioEmu, CryoVia, CryoFold, CryoPROS, EMInfo, Follow_Relion_Gracefully, Locscale, OutlierRemoval, Psi4, RosettaDDGPrediction, and xtb. See Software Changes below for complete details.

Five new members joined in the month of May: Lars-Anders Carlson from Umeå University, Ali Hamiche from Institute of Genetics, Molecular and Cellular Biology, Sam Li from Nanyang Technological University, Abdullah Al Mamun from Meharry Medical College, and Evan O'Brien from Johns Hopkins University School of Medicine. Welcome to our newest members!

For those who are new to SBGrid, a reminder about a few resources available to you:

Visit our wiki to learn more about getting started: https://sbgrid.org/wiki/getting_started

Register for personal installation manager credentials to manage software on laptops or desktops at home or in the lab: https://sbgrid.org/registration/register/

Submit a request for new or updated software that you would like to see added to the SBGrid collection: https://sbgrid.org/help/?tab=software

Override the default software version for a particular title to try out new features in a beta release or revert to an old version for reproducibility:  https://sbgrid.org/wiki/versions

NE-CAT is offering a two-day Data Collection and Processing Bootcamp at the Advanced Photon Source in Lemont, Illinois on July 24-25, 2025 (two days after the ACA Meeting in Lombard, IL). Bootcamp participants must be registered users of the APS and have or anticipate having crystals by the course date.

Full details: https://necat.chem.cornell.edu/data-collection-and-processing-bootcamp

Spots are still available for the Bootcamp; fill out this Google form to register: https://forms.gle/Lr39kFrGP2bYbA9M8

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:

- Caltech doctoral student Vida Storm Robertson highlighted a publication from SBGrid member Yvain Nicolet, at IBS Grenoble, in which the authors explore how bacteria make antibiotics. Read more: https://medium.com/sbgrid-community-news/how-microbes-make-designer-antibiotics-a16d41cb6de6

- Meharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a publication from the laboratory of Elias Lolis from Yale University School of Medicine that examines the immune protein MIF with an allosteric inhibitor, which can halt leukemia cell growth, offering a promising new strategy for treating AML.

Read more: https://medium.com/sbgrid-community-news/exploring-mif-inhibition-in-acute-myeloid-leukemia-f6aaa184677c

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: 

Jean-Philippe Julien from The Hospital for Sick Children Research Institute in Nature Structural & Molecular Biology: Structural elucidation of full-length Pfs48/45 in complex with potent monoclonal antibodies isolated from a naturally exposed individual; and Joost Snijder from Utrecht University in eLife: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry.

BioEmu 0.1.11 is a biomolecular emulator that samples from the approximated equilibrium distribution of structures for a protein monomer given its amino acid sequence using generative deep learning, providing inference code and model weights: https://github.com/microsoft/bioemu/releases.

CryoVia 1.0 is an image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs: https://github.com/philipp-schoennenbeck/CryoVia.

CryoFold 20250325 is a graphical user interface for the CryoFold method, which integrates several computational techniques (MAINMAST, Targeted Molecular Dynamics, MDFF/ReMDFF, and MELD) to determine protein structures and conformational ensembles from cryo-EM density maps:  https://github.com/SingharoyLab/CryoFold_GUI.

CryoPROS 1.0.1 is a computational framework specifically designed to tackle misalignment errors caused by preferred orientation issues in single-particle cryo-EM. By co-refining synthesized and experimental data and utilizing a self-supervised deep generative model, cryoPROS synthesizes auxiliary particles that effectively eliminate these misalignment errors through a co-refinement process: 

https://github.com/mxhulab/cryopros/tree/v1.0.1.

EMInfo 1.1 is a deep learning framework for detecting the secondary structures of proteins and the region of nucleic acids in a cryo-EM map: https://huanglab.phys.hust.edu.cn/EMInfo/ .

Follow_Relion_Gracefully 6 is a complete dashboard for easy interaction with your cryo-EM data in Relion, now with full #teamtomo support! It allows users to visualize and analyze data in real-time and includes job previews, enhanced data visualization, and the ability to download volumes directly from the dashboard: 

https://github.com/dzyla/Follow_Relion_gracefully?tab=readme-ov-file.

Locscale 2.3.0 is an automated tool for physics-informed cryo-EM map optimization (sharpening/density modification), improving interpretability using electron scattering properties derived from the map or an atomic model: https://github.com/cryoTUD/locscale.

OutlierRemoval 876474b is an implementation of outlier removal in cryo-electron microscopy (cryo-EM) datasets using radial profiles. The method focuses on removing outliers to enhance the quality of the 2D class averages and downstream analysis:

https://github.com/lovakap/OutlierRemoval.

Psi4 1.9.1 is suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of molecular properties that routinely performs computations with >2500 basis functions on multi-core machines: https://github.com/psi4/psi4

RosettaDDGPrediction is a Python package to run Rosetta-based protocols for the prediction of the ΔΔG of stability upon mutation of a monomeric protein or the ΔΔG of binding upon mutation of a protein complex and analyze the results: https://github.com/ELELAB/RosettaDDGPrediction

xtb 6.7.1 implements semiempirical quantum mechanical methods GFNn-xTB, their descendants, and corresponding composite schemes:

https://xtb-docs.readthedocs.io/en/latest/.

Boltz-1 1.0.0 introduces inference-time steering for improved physical quality of poses and CUDA kernels for faster and more memory-efficient inference and training. This version also adds a new cyclic flag for proteins in the input YAML, which tweaks relative positional encoding to significantly enhance predictions for cyclic peptides:

https://github.com/jwohlwend/boltz/releases/tag/v1.0.0.

CNS 1.3 release 9 now compiles for arm64 CPUs on macOS, with a significant boost in performance: https://cns-online.org/v1.3/.

cryoDRGN 3.4.4 adds Python 3.12 support, fixes batch iteration and dependency issues for interactive filtering, introduces a ⁠--shuffle-seed argument for improved reproducibility, migrates documentation fully to GitBook, and adds an alpha version of the ⁠analyze_convergence tool. Python 3.9 support is also deprecated: https://github.com/ml-struct-bio/cryodrgn/releases/tag/3.4.4.

MemBrain-Seg 0.0.8 fixes filtered mrcfile loading warnings, a logging type error, and adds a link to a Google Colab example notebook: https://github.com/teamtomo/membrain-seg/releases/tag/v0.0.8  

ModelAngelo 1.0.14 changes the pytorch version to stay in line with Relion: 

https://github.com/3dem/model-angelo/releases/tag/v1.0.14.

PyEM 0.66 is now available.

Relion 4.0.2 is the second and final maintenance release of the Relion 4.0 series. It provides bug fixes and some new features including --external_recosntruct as a flag for continued refinements, improved parallelization in relion_convert_to_tiff --only_do_unfinished, a repair to relion_reconstruct --ewald --newbox (e16f796), consistency in frame numbers (1-indexed) in relion_convert_to_tiff (0b03a6f), and  improved parallelization in relion_convert_to_tiff --only_do_unfinished: https://github.com/3dem/relion/releases.

Scipion 3.7.1, the latest version of this CryoEM image processing framework, is now integrated with SBGrid capsules to allow Scipion plugins to work with software in the SBGrid collection. For now only the Single Particle Analysis (SPA) plugins are available, but integration of tomography plugins is coming soon!

Topaz 0.3.8 was added.

XDS 20250430 addresses a small bias in the intensity estimation of weak reflections during the INTEGRATE step, particularly affecting weak data, and restores behavior similar to the 20230630 and 20250327 versions: https://xds.mr.mpg.de/html_doc/Release_Notes.html.

Xmipp 3.24.12.2 is the latest version and includes lots of new features for SPA, including a new installer and dependencies that make it easier to keep Xmipp updated in SBGrid:

https://github.com/I2PC/scipion-em-xmipp/releases.

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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