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Reposted by Oli Clarke

James A. Letts @lettsscience.bsky.social · 3h

Exciting new preprint from the Maldonado Lab @ucdavis.bsky.social
Structure of photosystem I from Giant Kelp!! First brown algae structure of a photosystem and the first structure of any protein from giant kelp a major primary producer, ecosystem defining species.
www.biorxiv.org/content/10.1...

Structure of Photosystem I-FCP from giant kelp uncovers drivers of antenna evolution across the red lineage

Brown algae and other red-algae-derived organisms such as diatoms are major contributors to global CO2 fixation via photosynthesis. To understand the photosynthetic function of brown algae, we obtaine...

www.biorxiv.org

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Derek Lowe @dereklowe.bsky.social · 5h

Absolutely true. And I’m glad he’s saying it.

AFP News Agency @en.afp.com · 16h

"It is going to be disastrous if this continues"

Nobel Prize physics laureate John Clarke says Trump cuts will 'cripple' US scientific research

u.afp.com/SmAy

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Oli Clarke @olibclarke.bsky.social · 5h

One of my very first placements as an undergrad was with Richard Robson! Growing MOFs with uranyl ions (which sadly failed to crystallize) and organoborate triangles (which worked). Was one of my first experiences with structure determination and I was hooked - so happy to see this!

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Milot Mirdita @milot.bsky.social · 1d

AFDB v6 is already available in Foldseek!

🚀 search.foldseek.com

foldseek databases Alphafold/UniProt50 afdb50 tmp
foldseek easy-search query.cif afdb50 res.m8 tmp --cluster-search 0/1 (Reps only / all 241M)

Thanks @ebi.embl.org and DeepMind for working with us to make it available to everyone.

EMBL-EBI @ebi.embl.org · 1d

We’re renewing our collaboration with Google DeepMind!

We'll keep developing the AlphaFold Database to support protein science worldwide 🎉

To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.

www.ebi.ac.uk/about/news/t...

🖥️🧬 #AlphaFold
@pdbeurope.bsky.social

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cryoEM papers @cryoempapers.bsky.social · 1d

ANTIDOTE: A Metadata-Driven Neural Network for Improving CryoEM 3-D Particle Sorting www.biorxiv.org/content/10.1101/2025.10.06.680814v1 #cryoem

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The Daum Lab @daumlab.bsky.social · 2d

Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail

This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.

www.science.org

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Sjors Scheres @sjorsscheres.bsky.social · 3d

If you are interesting in developing new algorithms for #cryoEM as a #PhD student or as a #postdoc, then do email or DM me. We have exciting opportunities coming up.

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Oli Clarke @olibclarke.bsky.social · 2d

Turtle yoga in central park 🧘‍♂️

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Oli Clarke @olibclarke.bsky.social · 3d

Also might be worth trying sym expansion, local refinement & Class3D w/out alignments, to test for unexpected pseudosymmetry

Oli Clarke @olibclarke.bsky.social · 3d

Have you tried foldseek using the poly-A from modelangelo as a search model? It does look similar to a phage tail at first glance, e.g. the C6 one here: www.cell.com/structure/fu...

Cryo-EM structure of flagellotropic bacteriophage Chi

Sonani et al. report the structure of bacteriophage χ using cryo-EM, revealing its capsid, neck, tail, and tail-tip organization. Unique proteins in the neck and tail tip, including a trimeric assembl...

www.cell.com

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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 3d

Another day, another paper by the Baker's lab

bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 5d

De novo design of RNA and nucleoprotein complexes https://www.biorxiv.org/content/10.1101/2025.10.01.679929v1

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Oli Clarke @olibclarke.bsky.social · 3d

Also - for the more flexible filaments, thinking mostly about the weird lysozyme tube - did you try helical sym expansion followed by local refinement with a mask around the central section? I’ve found this to help quite a lot with flexible filaments

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Oli Clarke @olibclarke.bsky.social · 3d

… and I also think there is a pretty balanced discussion in this preprint of the limitations of CS with respect to RELION for processing amyloid samples (and validation issues etc)

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Oli Clarke @olibclarke.bsky.social · 3d

Fantastic work Jan! Have you had a go at the FIA filament from the BLUSH paper? I haven’t been able to get that one to go in CS, but I am far from an amyloid expert

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Oli Clarke @olibclarke.bsky.social · 3d

I think this is a bit of a false dichotomy Sjors - not everyone needs to (or is able to) develop new algorithms, and there is a place for learning how to use existing software optimally for specific types of samples, whether closed source or not - I don’t see why this has to be an either/or…

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Jan-Hannes Schaefer @jhschaef.bsky.social · 3d

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...

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cryoEM papers @cryoempapers.bsky.social · 4d

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail pubmed.ncbi.nlm.nih.gov/41042861/ #cryoem

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Edward T Eng @edwardteng.bsky.social · 4d

Muyuan Chen has turned structural biology into an immersive experience with his new video game Meowtabolism, now available on Steam.
Try the demo here: store.steampowered.com/app/4045010/...
Give Muyuan feedback: steamcommunity.com/app/4045010
#ScienceGaming #StructuralBiology #CryoEM #STEMOutreach

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bioRxivpreprint @biorxivpreprint.bsky.social · 8d

GABAA receptor gating imaged on the millisecond timescale https://www.biorxiv.org/content/10.1101/2025.09.29.679341v1

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Oli Clarke @olibclarke.bsky.social · 4d

Bit of a mix - have bought 4 workstations over the years connected by a NAS. Our latest is 4xA6000, threadripper, 512G RAM, as much fast SSD as I could fit - have been happy with that one

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Oli Clarke @olibclarke.bsky.social · 4d

Convergence behavior is very case dependent - e.g. iPKAc converges quite fast (sidechains apparent by ~iter1200 and gets progressively better) whereas in situ ribosomes stay very low resolution for 5400 iterations and then suddenly converge (see earlier post)

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Oli Clarke @olibclarke.bsky.social · 4d

… after alignment (Align3D) with update particle orientations on.

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Oli Clarke @olibclarke.bsky.social · 4d

The other thing is I would often try with/without enforce non-negativity (sometimes one gives a better result than the other)

Also if you want to be confident about res estimation, you can split the data in half, run ab initio on both (w same seed), then use the matched ab initios as half sets…

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Oli Clarke @olibclarke.bsky.social · 4d

Really depends - you’ll need to play with the high res limit depending on the data - if you are seeing a lot of random spikes, you might want to back it off a tad.

If it has already seen all the data (epoch >1) and you are happy with the map, you can safely kill, mark complete and move to local ref

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Oli Clarke @olibclarke.bsky.social · 4d

Haven’t tried with signal subtraction, but I have tried on subparticles cropped out from larger complexes and it worked there, so worth a try!

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