Some questions for our structural biology community: What protocols do you think would be useful to have? Do you prefer to watch step-by-step videos, or follow written instructions? Of course, not everything has to be a video, but certain workflows are simply best documented on video #protocols

Structural Biology Communications@actacrystf.iucr.org · 6d ago

A new type of article for Acta F: Protocols The purpose of this new category is to provide to the reader procedures that are sufficiently detailed so other researchers can reproduce the described workflow. Find out more in 'Show me how it's done: introducing Protocols': doi.org/10.1107/S205...

Bacteriophage tails co-enrich with ex vivo amyloids from amyloidosis patients. Cryo-EM reveals Siphoviridae tail tube protein in ALys and AL amyloid extract. Do phages interact with human amyloids? @landerlab.bsky.social @nanigrotjahn.bsky.social & Kelly Lab #cryoEM #b3d doi.org/10.64898/202...

New paper out in @actacrystf.iucr.org! We benchmarked cryoSPARC for amyloid helical reconstruction: ease of use over RELION, but amyloid-specific development still needed & software interoperability remains a problem. @landerlab.bsky.social Kelly Lab @scripps.edu doi.org/10.1107/S205...

We are pleased to release an update to this pre-print! Includes (1) proof-of-principle experiments on ultrasonic excitation during plunge vitrification, (2) cryo-ET characterisation of the effect, (3) and insights into grid/ice quality following ultrasonic excitation during vitrification.

This is the kind of work, published today, that should be fully supported and prioritized at the highest level. Currently, there is no vaccine vs the Ebola Bundibugyo virus, the source of a major outbreak www.pnas.org/doi/10.1073/...

Try this new online training game from Leandro F. Estrozi designed for newcomers in structural biology, with a focus on cryo-EM and cryo-ET map interpretation: rico.ibs.fr/helixplo...

In our new work from the Kelly, Ye & @landerlab.bsky.social , we link ATTR cardiomyopathy to microangiopathy. Increased capillary permeability exposes components of the vascular basement membrane to misfolded TTR. Work led by Joe Donnelly. #amyloidosis #cryoem #b3d doi.org/10.1161/JAHA...

We identified the maltoside detergent DM as an effective and easy solution to address preferred orientation in cryo-EM. Helped me switch from graphene grids. Special congrats to Maria Rafiq! @landerlab.bsky.social @nanigrotjahn.bsky.social @wisemanlab.bsky.social #cryoEM doi.org/10.64898/202...

We're excited to announce the beta-release of #RELION-5.1! 🥳 This release has important updates on our #amyloid processing pipeline, as described in this preprint: doi.org/10.64898/202... There are also some tweaks for #teamtomo. #OpenSoftwareAcceleratesScience

Great to see one of my PhD projects out on bioRxiv. We report "A dual sensor regulates P-glycoproteins structural plasticity." Congrats to Michael Kamel for doing the heavy lifting from @arnemoeller.bsky.social & Urbatsch Lab. doi.org/10.64898/202... #b3d #cryoEM

For obvious reasons, we need a Paceometer! #endroadrage doi.org/10.1017/S193...

I've written a review on what I think is an extremely exciting direction in cryo-EM: Cryo-EM of endogenous membrane proteins in their native lipid bilayer Open access in Quarterly Reviews of Biophysics: doi.org/10.1017/S003...

The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....

Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...

Thanks, I guess we all needed this.

Alice Auersperg@auersperga.bsky.social · 7mo ago

Our new paper (with @biotay.bsky.social) is out and on the cover story of @currentbiology.bsky.social !!!! Veronika, a Carinthian mountain cow flexibly uses a “multi-purpose tool” to scratch herself. A video and more information will follow in the comments. www.cell.com/current-biol...

In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...

Thanks to @actacrystf.iucr.org for highlighting our smart 2D selection tool CryoSift. You can test it yourself here cryosift.org

Jon Agirre@glycojones.bsky.social · 8mo ago

New interview alert! We had a chat with Mike Cianfrocco, Scott Stagg and Jan-Hannes Schäfer about their CryoSift tool – details in the thread. www.youtube.com/watch?v=ROlc...

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier! I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!

Sjors Scheres@sjorsscheres.bsky.social · 9mo ago

At some point, Doppio will replace relion's gui. Already you can do more in Doppio than in relion! 🤩

CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection

CryoSift is a CNN-based tool that assesses the quality of 2D class averages. The incorporation of CryoSift into cryoSPARC workflows enables automated particle-stack cleaning.

doi.org

Jan-Hannes Schaefer@jhschaef.bsky.social · last yr.

Check out our new preprint from the @landerlab.bsky.social, Stagg-Lab and Cianfrocco-Lab: CryoSift - An accessible and automated CNN-driven tool for cryo-EM 2D class selection www.biorxiv.org/content/10.1... Happy testing: cryosift.org #cryoEM #CNN

Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale #ElectronMicroscopy #CryoEM #TimeResolvedStudies ... #IUCr https://journals.iucr.org/paper?S2052252525008838

`Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale

The development of methods for low-cost time-resolved cryo-EM using an on-grid mixing strategy is described.

journals.iucr.org

Excited to share a new chapter of my scientific journey in Chris Russo's group — developing a way to freeze proteins faster than they diffuse, paving the way for cryo-EM without air–water interface damage.

MRC Laboratory of Molecular Biology@mrclmb.ac.uk · 10mo ago

Chris Russo and Anastasiia Gusach have developed a new method to prepare #cryoEM samples that avoids protein damage during freezing Read more: www2.mrc-lmb.cam.ac.uk/a-new-method... #LMBResearch

🚀 Introducing fully automated data processing for repeat-target #cryoEM. Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention. Preprint: www.biorxiv.org/content/10.1...

Thanks @odedrechavi.bsky.social. Even without explicit coverage of structural biology, it did a great job as Reviewer #0 on my latest preprint. Highly recommend www.qedscience.com

q.e.d Science

Critical Thinking AI for constructive criticism and science evaluation

qedscience.com

Oded Rechavi@odedrechavi.bsky.social · 10mo ago

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

Helical Reconstruction of Amyloids in cryoSPARC? We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social. Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...

‪We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends landaulabcssb.bsky.social

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup). A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.

Sjors Scheres@sjorsscheres.bsky.social · 11mo ago

These results are truly impressive! But I do worry that #cryoEM is moving into a phase where progress is made by optimizing parameter settings for black box programs. The devil is often in the details, and I am not sure how this could be implemented in #relion, as stated, without more info.

❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 11mo ago

Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification https://www.biorxiv.org/content/10.1101/2025.09.14.676144v1

Another successful approach to the same problem as HR-HAIR! 🤩 I wonder if a combo might be worth a try - use one frequency band to get perfectly centered particles using 2DTM, then re-estimate orientations using HR-HAIR with a non-overlapping frequency band?

cryoEM papers@cryoempapers.bsky.social · 11mo ago

Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoEM

A great resource. One highlight for me is: "One of the best things about structural biology is visualizing what you are discovering."

Stephanie Wankowicz@stephanieaw.bsky.social · 11mo ago

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...