Neat ! Thanks, I will install it tomorrow if I have the time! Cheers,

Will do. I'll look into the coot log to see if it says anything.

I also put the file in /.coot-preferences/

Haha I tried...and also put that file in it as well....

So my coot_preferences.py file is located in ~/.coot/ so this is where I put the trimmings file. ~/.config/Coot/ doesn't exist.

I don't see any differences, the new menus and new mouse behavior doesn't take effect.

Thanks,

Hey Oli, thanks for those very nifty tools (including the ChimeraX one). I have Coot 1 on Tahoe Mac OS, installed through SBgrid (our IT department does that) and I can't find the right path to put the .py script for it to be recognized by Coot. Any insight on this?

Great figures, and I love when the preprint is formatted like that. Great work, reading right now!

Fun collaboration with the Herzik lab! Very cool to see #TeamTomo + STA directly capture the effects of the AWI at the single-particle level. we know it’s happening, but it’s striking to see it so clearly!

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

More evidence also that the federal administration is NOT pursuing actual criminal activity- they have forced out the very prosecutors who were working on the social services fraud cases that had been the proclaimed casus belli for sending federal forces to MN.

How "Free Speech Culture" Is Killing Free Speech: Part One Blurring The Lines Between Official Censorship And Individual Criticism Built The Intellectual Foundation For Trump's Assault On Free Expression

So many lucid points below. Incl on how to think abt free speech issues brought up by backlash on campuses when illiberal right-wingers are invited to speak. Also, and this has agitated me since Jan 2025: those who railed against cancel culture seem at ease with state-enforced speech restrictions.

Yes, It’s Fascism Until recently, I thought it a term best avoided. But now, the resemblances are too many and too strong to deny.

I’m no historian, nor political scientist, and the term is definitely overused, but…

How do you get it to change colors??? Ours only does green when cold and white when warm

Makes sense! looks like limestone

Where is that roof one with the city in the back drop? Cool contrast!

Ah don't get me started!I miss climbing in the Sierras so much! Still waiting for my back to get better after my injury...

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.

Lattices is an optimal way of packing so perhaps it just packs this way to cram as many as possible on the membrane in a stable way....Anyways, always impressed with the Engel lab papers! In-situ structure work is the best kind of in-situ

A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾

Very impressive tomograms. Those lattices on the thylakoid membranes...could almost do 2D xtallography...Beautiful work!

It has also worked for us for a small protein without using any scaffolding. Although we are careful with the model, we are quite impressed by the map quality achieved as we were able to dock it a refine it pretty well. With that said, we are cautious and eager to hear the whole story :)

Absolutely!

Very interesting. Thanks

Love the drawing!

If you are thinking about the future of structural biology, we are too! Our two cents (Jürgen Plitzko and I) just got published online here: authors.elsevier.com/sd/article/S...

Research Xu Lab of Computational Biology

New Title Alert: AITom- an open-source platform for AI driven cellular electron cryo-tomography analysis.

Learn more here: buff.ly/LLGhjvY

#SBGrid #SBGridSoftware #StructuralBiology

I tried that but what worked the best was to germinate on agar germinating medium, then resuspend them gently and pipette them on grid. Not trivial but doable.

(PDF) Cryo-electron tomography methods applied to plant science PDF | FIB milling application on whole plant cells | Find, read and cite all the research you need on ResearchGate

Also, I made a poster about this unpublished data: www.researchgate.net/publication/...

Congratulations!

New preprint: In situ Architecture of #Plasmodesmata.

Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.

🔗 doi.org/10.1101/2025...

🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM