SBGrid Newsletter: May 2026

Dear Consortium Members and Affiliates,

Our Consortium update for May includes a new date coming soon for the Ais and Pom webinar planned for June, a recording of our May PyMOL webinar, a software push with 19 updates and three new titles, three new members to welcome, community announcements with event listings from Instruct-ERIC and a position posting from Antonina Roll-Mecak's laboratory, and two publication highlights featuring work from the laboratories of Crina Nimigean and Huanhuan Joyce Chen.

Our June webinar is postponed due to a scheduling conflict. We'll post a new date soon to hear from Mart Last on the tomography tools Ais and Pom. In case you missed Jarret Johnson's presentation on visualization and CryoEM in PyMOL earlier this month, you can watch the recording on the SBGrid YouTube Channel. 

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

Send us your suggestions for the 2026-2027 software webinar series.

June 9: (New Date Coming Soon) 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 AlphaFold3, autoPROC, BoltzGen, Buster, CCP4, ChemEx, COOT, cryoCAT , DIALS, Maxit, MotionCor3, OpenFreeEnergy, OpenMM, PowerFit, pytom-match-pick, TOMOMAN, Topaz, Volume_Seg_Tool, and Warp along with three new titles: Germinal, miss-alignment, xds-zcbf

See Software Changes below for complete details.

Three new members joined in the month of May: the CryoEM Facility at Michigan State University led by Sundhar Subramanianat, the Nanoimaging Platform at Institut Pasteur led by Matthijn Vos, and Sttephanie Wankowicz in her new lab at Astera Institute. 

Welcome to our newest members!

Instruct Course on Calorimetric and Spectroscopic Characterization of Biomolecules 

Sept 7-11, 2026 | Brno, Czechia

Organized in collaboration with Anamet and Specion

Register here: https://www.ceitec.eu/instruct-course-on-calorimetric-and-spectroscopic-characterization-of-biomolecules/a5545

Instruct-ERIC hands-on workshop on: Advanced cryo-FIB-SEM methods  

Nov 9-13, 2026 | Heidelberg, Germany

Organized by the EMBL Imaging Centre

Register here: https://www.embl.org/about/info/imaging-centre/events/instruct-eric-hands-on-workshop-on-advanced-cryo-fib-sem-methods-09-13-11-2026/#vf-tabs__section-a7ff03a1-a072-4030-b285-e8941fc232f0

Postdoctoral Fellow | Antonina Roll-Mecak Laboratory | NIH

Advance our knowledge on mechanisms of cytoskeletal regulation, with a focus on the tubulin code. Projects leverage a powerful combination of in vitro reconstitution, high-resolution cryo-EM, and cryo-electron tomography in iPSC derived human neurons to reveal how the cytoskeleton is built, regulated, and remodeled. For recent examples of work from our lab see Zehr et al., NSMB 2026; Whittaker et al., MBoC 2026; Chen et al., Nature 2024. The successful candidate will obtain excellent training in cryo-EM, cell biology, neural stem cell culture techniques, and biochemistry, and work with the Advanced Imaging & Microscopy center at the NIH as part of a collaborative co-mentored experience. We are looking for Ph.D. graduates with backgrounds in either of these areas: biochemistry, structural biology, cytoskeletal motors, and single molecule biophysics. Please send your CV, a one-page research experience summary and contact information of three references to Antonina@nih.gov, and specify “Tubulin code structural cell biology” in the subject header. 

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:

Student contributors highlight member publications with a focus on science education and demonstrating how structural biology and preclinical science connect to medicine. 

Fisk University student Cariuna Ellison's highlight features a Nature Communications publication from the laboratory of Crina Nimigean at Weill Cornell Medicine in which the authors describe the precise conditions and resulting mechanisms that result in thermosensitivity in a bacterium.[Learn more.]

- Meharry Medical College student Mudia Ikoba highlighted a publication that appeared in Science Advances from SBGrid member Huanhuan Joyce Chen and colleagues at The University of Chicago, exploring the mechanism underlying pulmonary neuroendocrine cells’ response to oxidative stress. [Learn 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:  https://data.sbgrid.org/

SBGrid operations are primarily funded with member fees and grants, so we are grateful when you can acknowledge SBGrid in manuscripts, preprints, and related work where appropriate. We recommend the following language for inclusion in the methods section of your publications that report results obtained with SBGrid supported software:

Software: Computational analyses were performed using the SBGrid software environment, which provides curated, version-controlled structural biology applications and reproducible execution environments across platforms (Herre et al., 2024).

Software and computational environment: All computational analyses were carried out using the SBGrid software environment, which provides curated, version-controlled access to structural biology software and manages dependencies to support reproducible research. Software execution was supported through the SBGrid Capsules framework, which standardizes application environments and workflows across platforms, as described in Herre et al. (2024).

Reference: Herre C, Ho A, Eisenbraun B, et al. (2024). Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection. Acta Crystallographica D, 80. 

Link to article:https://journals.iucr.org/d/issues/2024/06/00/gm5107/index.html

SBGrid logo for use on the acknowledgements slide of presentations.

SBGrid's eLife and Acta Crystallographica D publications received five new citations since our last reporting, from these SBGrid members and contributing developers:

Seth Darst The Rockefeller University in Molecular Cell: Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity. 

https://www.cell.com/molecular-cell/fulltext/S1097-2765(26)00209-1

Brandt Eichman from Vanderbilt University in EMBO Reports: DNA binding and lesion recognition by the bacterial interstrand DNA crosslink glycosylase AlkX.

https://link.springer.com/article/10.1038/s44319-026-00785-6

Christopher Garcia from Stanford University School of Medicine in Nature Biotechnology: Deep peptide recognition profiling decodes TCR specificity and enables disease-associated antigen discovery.

https://www.nature.com/articles/s41587-026-03128-x

Lynne Howell from University of Toronto in Journal of Biological Chemistry: Bacillus cereus PelADA is a polysaccharide de-N-acetylase required for Pel-dependent biofilm formation. 

https://www.sciencedirect.com/science/article/pii/S0021925826019940

Dirk Slotboom from University of Groningen in Journal of Biological Chemistry:  NAAC: An affinity chromatography strategy enabling characterization and quantification of influenza. 

https://www.sciencedirect.com/science/article/pii/S0021925826020107

Germinal 20260512 is a pipeline for designing de novo antibodies against specified epitopes on target proteins. The pipeline follows a 3-step process: hallucination-based on ColabDesign, selective sequence redesign with AbMPNN, and co-folding with a structure prediction model. Germinal is capable of designing both nanobodies and scFvs against user-specified residues on target proteins.

https://github.com/SantiagoMille/germinal/tree/main

miss-alignment 0.1.6 (new) is a GPU-based tool for improving cryo-ET tilt-series alignments, designed to run from an initial eTomo/WarpTools patch-tracking alignment. It provides a command-line workflow for training and reconstruction across one or more GPUs, with guidance for WarpTools and single-node SLURM use.
https://github.com/warpem/miss-alignment/tree/main

xds-zcbf is an XDS plugin for fast reading of cbf.gz files. While XDS can read cbf.gz files on its own, this plugin eliminates the need for multiple file system accesses by way of direct calls to zlib, thus speeding up the processing.

https://git.embl.org/nikolova/xds-zcbf 

AlphaFold3 3.0.2 adds out-of-the-box support for NVIDIA Blackwell GPUs, improves MSA search performance with support for sharded Jackhmmer/Nhmmer databases, and reduces memory use in several workflows. It also adds user-facing options for external CCD files, forcing output into an existing directory, saving distograms, and compressing large mmCIF/confidence outputs, alongside fixes for template handling, custom CCD validation, MSA pairing preservation, and output naming.

https://github.com/google-deepmind/alphafold3/releases/tag/v3.0.2

autoPROC 20260424 includes a new recommended XDS version (20250714), new tools for wavelength/energy consistency checking, Bruker/SFRM-to-XDS metadata setup, and MTZ filtering of Inf/NaN or extreme values before downstream crashes. It adds ESRF Lima2 VDS support in hdf2mini-cbf, improves imginfo and Durin handling of HDF5 metadata variants, expands STARANISO capabilities and fixes, and updates workflow, detector, and beamline support for several facilities.
https://www.globalphasing.com/autoproc/ReleaseNotes/ReleaseNotes-autoPROC_snapshot_20260424.txt

BoltzGen 0.3.2 fixes handling of binding_types so that binding entries are no longer dropped when combined with not_binding.

https://github.com/HannesStark/boltzgen/releases/tag/v0.3.2

Buster 20260424 includes a new -restraints mechanism for editing BUSTER refinement restraints, a HighRes.macro for very-high-resolution refinement, and initial DiSCaMB support for TAAM-based structure-factor and gradient calculations. Grade2 gains --ccd output for generating PDB Chemical Component Dictionary CIF files, switches CIF handling to Gemmi, improves covalent ligand/PTM documentation, and restores compatibility with CSD releases through 2026.1. This release also fixes cover aB_autorefine -noRIG behavior, RhoFit plane handling, AceDRG dictionary parsing, PubChem lookup, and several geometry/restraint issues.

https://www.globalphasing.com/buster/ReleaseNotes/ReleaseNotes-BUSTER_snapshot_20260424.txt

CCP4 9.0.015 refreshes core crystallography components including Gemmi 0.7.4, Servalcat 0.4.128, Dimple 0.7, ModelCraft 6.1.0, MetalCoord 0.2.13, Coot API 1.1.20, Coot-1 1.1.20, ccp4i2 2.6.x, DUI2 2026.3.20, Pointless 1.15.2, and Aimless 0.8.3. This update also adds NucleoFind and a new ccp4i2 task for predicting nucleic-acid features in maps, adds an AREAIMOL task for solvent-accessible surface area calculations, updates monomer/link handling, and includes fixes for anomalous merged-file reindexing, standard monomers, covalent links, and AFDB version checks.

https://www.ccp4.ac.uk/ccp4-9-0-updates

ChemEx 2026.05.1 is an infrastructure-focused release that resolves type-checking issues and refactors internal data handling to use idiomatic Pydantic v2 initialization. No major user-facing workflow changes are listed for this release.
https://github.com/gbouvignies/ChemEx/releases/tag/v2026.05.1

COOT 1.3.1 resolves a stability issue within the Sequence View, building on the significant features introduced in version 1.3. Notable additions include AlphaFold refinement workflows, cryo-EM molecular placement, map caps for sliced views along with improved ligand browsing and new validation tools.

https://github.com/pemsley/coot/releases/tag/Release-1.3

cryoCAT 0.7.1 adds support for TANGO along with improvements to stability and documentation.

DIALS 3.28.1 fixes several issues across the DIALS, dxtbx, and xia2 workflows and  improves handling of some NXmx Eiger filewriter metadata cases when dependencies are missing.
https://github.com/dials/dials/releases/tag/v3.28.1

Maxit 11.400 is the new default. No changelog is available.

https://sw-tools.rcsb.org/apps/MAXIT/source.html 

MotionCor3 1.2.4 fixes a bug that caused errors in the generation of dose-weighted micrographs including DW and DWS.

https://github.com/czimaginginstitute/MotionCor3/pull/33 

OpenFreeEnergy 1.11.0 adds membrane-system support across several OpenMM-based protocols, including PlainMD, RelativeHybridTopology, SepTop, and AbsoluteBinding workflows, with CLI support through openfe plan-rbfe-network. It also adds resume support for PlainMD and SepTop, improves SepTop validation and analysis handling, updates protocol documentation, and fixes restart behavior where small force-parameter precision differences across machines could block simulation resumption.

https://github.com/OpenFreeEnergy/openfe/releases/tag/v1.11.0

OpenFreeEnergy 1.11.1 is a minor update that improves responsiveness for slow CLI commands along with some installation-documentation updates.
https://github.com/OpenFreeEnergy/openfe/releases/tag/v1.11.1

OpenMM 8.5.1 is a patch release with fixes for template constraint assignment, minimizer energy comparison precision, worker-thread force handling, and pressure calculations in MonteCarloFlexibleBarostat.
https://github.com/openmm/openmm/releases/tag/8.5.1

PowerFit 5.0.0 adds a CUDA backend for GPU acceleration, batched GPU rotations, and planned FFT reuse. There are also changes to progress-bar behavior, now hidden by default and enabled with `--progressbar`, removes `--no-progressbar`, and fixes to the handling for some CIF files missing atom charge columns.

https://github.com/haddocking/powerfit/releases/tag/v5.0.0

pytom-match-pick 0.13.0 changes Warp XML tilt-angle handling by multiplying imported tilt angles by -1, which may affect workflows using Warp metadata. It also improves split-job efficiency by generating common template and tomogram filters once, and fixes tutorial tests for updated Dataverse download naming.
https://github.com/SBC-Utrecht/pytom-match-pick/releases/tag/0.13.0

TOMOMAN 0.9_20260505 fixes imod reconstruction, adds an option to output aligned stacks for AreTomo, and fixes the relion_motioncorr (Relion 5) task for writing odd/even stacks. 

https://github.com/wan-lab-vanderbilt/TOMOMAN/commits/master/ 

Topaz 0.3.19 and 0.3.20 are now available with fixes to dataloader bugs that limited worker usage and new options to preload training data into memory, with an automatic mode that preloads when the dataset fits comfortably in available memory. The denoise command also now returns paths by default rather than image lists, which should make downstream handling clearer.
https://github.com/tbepler/topaz/releases/tag/v0.3.19

Volume_Seg_Tool v0.12.0 improves performance and accuracy. It also supports prediction files larger than 4 GB and adds automatic mid-visualization generation, avoiding the need to prepare an image manually.
https://github.com/fgdfgfthgr-fox/Volume_Seg_Tool/releases/tag/v0.12.0

Warp 2.0.0dev39 includes migration of the backend framework from .NET 8 to .NET 10, a CUDA Toolkit Upgrade from 11.8 to 12.9, and a new requirement for NVIDIA driver version >= 525.60.13 supporting CUDA 12.x. Additional improvements include modifications to internal build and runtime environment scripts (such as warp_build.yml) to align with the new .NET 10 runtime and CUDA 12.9 requirement, as well as compatibility and stability maintenance.

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.

Learn more about SBGrid

- Consortium website: https://sbgrid.org

- Supported software: https://sbgrid.org/software/

- Report software bugs: sbgrid.org/bugs

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