Cooty McCootFace @cootymccootface.bsky.social · 03/04/2026Quick Demo of Agentic Coot www.youtube.com/watch?v=NkBA... (Yes, there is still work to do.)youtube.comAgentic Coot working with ClaudeYouTube video by Paul Emsley 082
Cooty McCootFace @cootymccootface.bsky.social · 03/04/2026This is the correct Release Notes for 1.2 pemsley.github.io/coot/blog/20...pemsley.github.ioRelease 1.2Coot 1.2 Released 1st April 2026 010
Cooty McCootFace @cootymccootface.bsky.social · 03/04/2026Coot 1.2 released With side-by-side stereo and Agentic Coot pemsley.github.io/coot/blog/20... pemsley.github.io/coot/blog/20... 3285
Cooty McCootFace @cootymccootface.bsky.social · 28/03/2026This is cool. A hover-over popup with the chemical diagram would also be cool. I'll see what I can do. 110
Cooty McCootFace @cootymccootface.bsky.social · 28/03/2026FYI to the public (not to Oli): the visual effect is more clean and impactful that it seems given this video compression. 020
Cooty McCootFace @cootymccootface.bsky.social · 16/03/2026Not yet. I need to teach it about servalcat and ligand fitting. 000
Cooty McCootFace @cootymccootface.bsky.social · 15/03/2026Note that you will need to have used pip to install FastMCP in the python that you use to run the MCP bridge (if that was not obvious). 000
Cooty McCootFace @cootymccootface.bsky.social · 15/03/2026Well... basically, you just add the Coot MCP as a new connector in Claude Desktop and then start the RPC server in Coot and then get going. But... I should write a blog post giving more details. 120
Cooty McCootFace @cootymccootface.bsky.social · 15/03/2026You can now make attractive-looking, dynamic, interactive in-line graphs in Claude Desktop using Agentic Coot (HEAD, not release that is - for the moment) 100
Cooty McCootFace @cootymccootface.bsky.social · 05/06/2025Coot Release 1.1.16 o FEATURE: Local B-factor display o FEATURE: Built-in logging (started) - view it by clicking the "Log" button o FEATURE: Anisotropic probability radius scaling o CHANGE: Boron atoms are now pinky-beige (like Jmol) #coot 093
Cooty McCootFace @cootymccootface.bsky.social · 01/04/2025Coot 1.1.15 Released Coot is 21 today! - Drag and Drop added (drop target) - Vertex gradients for map normals (smoother maps) - Fixed atoms are now draggable! - Fix and Unfix atoms now fixed! - Select Map dialog fixed - Merge Molecules dialog fixed - Trackpad zooming fixed 1281
Cooty McCootFace @cootymccootface.bsky.social · 19/03/2025Is the symmetry problem related to you Github question? 100
Cooty McCootFace @cootymccootface.bsky.social · 17/03/2025Coot 1.1.14 has been released! Coming to homebrew and flatpak soon! - Clark & Labute comes to Coot 1, Moorhen & chapi! (svg, 2D ligand environment view) - Solid Symmetry (symmetry that you can see!) - PAE plot for AlphaFold models #coot #molmatinf 02710
Cooty McCootFace @cootymccootface.bsky.social · 15/03/2025Just to be clear, I mean this image is freely reproducible - not the Science paper! 000
Cooty McCootFace @cootymccootface.bsky.social · 15/03/2025Human PINK1 at a TOM-VDADC array Structure of the Week/Month/Year(?)! 9eih. Sylvia Callegari...David Komander, Science 13 March 2025. #coot Fancy mode Copyright/license-free - i.e. freely reproducible. Coot 1.1.14 coming soon! 161
Cooty McCootFace @cootymccootface.bsky.social · 14/03/2025Solid-modelled symmetry atoms, so that you can see symmetry on macOS. Before and after Coot 1.1.14 coming soon! # coot 0141
Cooty McCootFace @cootymccootface.bsky.social · 09/03/2025You've probably got your agenda all sorted, but if you have room for a guest lecture @olibclarke.bsky.social could give you a good Coot seminar. 010
Cooty McCootFace @cootymccootface.bsky.social · 09/03/2025Coot-1 lives in the "coot_py3" directory in a CCP4 distribution. 100
Cooty McCootFace @cootymccootface.bsky.social · 08/03/2025Alphafold PAE plot added to Coot 1! Coot 1.1.14 coming soon! #coot 1140
Cooty McCootFace @cootymccootface.bsky.social · 02/03/2025You can represent atom selections as Metaballs in Moorhen Models → + → Style → Metaballs #moorhen 030
Cooty McCootFace @cootymccootface.bsky.social · 25/02/2025Coot from Homebrew has been updated! Yay Yoshitaka Moriwaki! 020
Cooty McCootFace @cootymccootface.bsky.social · 25/02/2025There's still lots of (very dull) work for us to do before we can robustly write modern mmCIF. 120
Cooty McCootFace @cootymccootface.bsky.social · 24/02/2025Coot 1.1.13 Released SSM Superpose works! NCS Ghosts works! CA label tracking on "spacing" through chain! #coot 180
Cooty McCootFace @cootymccootface.bsky.social · 20/02/2025After years of (off and on) effort, Coot 1 finally compiles and runs on Alma Linux! 0110
Cooty McCootFace @cootymccootface.bsky.social · 12/02/2025Coot 1.1.12 Released: Graphics viewport scaling, Acedrg Link, HOLE and several fixes pemsley.github.io/coot/blog/20...pemsley.github.ioRelease 1.1.12Release 1.1.12 o source tar: 020
Cooty McCootFace @cootymccootface.bsky.social · 07/02/2025HOLE-y! An implementation of Oliver Smart's HOLE now available in Coot 1 Linear Gramicidin D - 2y5m - behold the lipid phase! Coot 1.1.12 out soon #coot 080
Cooty McCootFace @cootymccootface.bsky.social · 06/02/2025QED: Quantifying the chemical beauty of drugs: pmc.ncbi.nlm.nih.gov/articles/PMC...pmc.ncbi.nlm.nih.govQuantifying the chemical beauty of drugsDruglikeness is a key consideration when selecting compounds during the early stages of drug discovery. However, evaluation of druglikeness in absolute terms does not adequately reflect the whole spec... 010
Cooty McCootFace @cootymccootface.bsky.social · 06/02/2025(I made a mistake, it's an ASP, not a GLU). A N in a pyridine is an acceptor, the trick is the see that although superficially the types are OC (acceptor) for OD1 and OD2, the side-chain is actually an acid! And hence a donor. The crystal was at pH5.4, which supported protonation of ASP. 000
Cooty McCootFace @cootymccootface.bsky.social · 05/02/2025Coot's Ligand Builder now has dark-mode icons and dynamic QED scoring... 1.1.12 out soon! #coot 190
Cooty McCootFace @cootymccootface.bsky.social · 01/02/2025Moorhen Gallery has gone live! Click on an image and Moorhen will download into your browser the data, model and session files to reproduce the figure - so you can see how it's made. Get in touch with @lulu_catapano in the other place if you want to make a contribution to the gallery! 073
Cooty McCootFace @cootymccootface.bsky.social · 26/01/2025Quiz Question! The glutamic acid side-chain and the LLP ligand from 1ajs fit their density nicely but the contacts on the ligand are unhappy (almost thinking the interaction is a clash). What's going on?/Why is Coot unhappy? 300
Cooty McCootFace @cootymccootface.bsky.social · 25/01/2025Coot's new Acedrg Link interface Coot 1.1.12 out soon! #coot 030
Cooty McCootFace @cootymccootface.bsky.social · 25/01/2025Coot no longer turns your ligand into a molten globule when you use a dictionary with no restraints! (thanks for the prompt, L.Masso) Coot 1.1.12 out next week! #coot 060
Cooty McCootFace @cootymccootface.bsky.social · 25/01/2025Puzzling green blob you have there... why didn't the refinement program just move those atoms down a bit...? 110
Cooty McCootFace @cootymccootface.bsky.social · 17/01/2025After looking at EM maps for months, the Holton "Untangle Challenge" map looks so pretty... 030
Cooty McCootFace @cootymccootface.bsky.social · 16/01/2025A few slides from Lucrezia Catapano's recent CCP4 Study Weekend presentation - there will be a CCP4 YouTube video at some stage 061
Cooty McCootFace @cootymccootface.bsky.social · 10/01/2025Lucrezia Catapano has a style all her own when giving a Coot presentation... 020
Cooty McCootFace @cootymccootface.bsky.social · 13/12/2024Coot has a built-in Poisson–Boltzmann solver and can make electrostatic surfaces quite snapily these days (8r96 in this example) #coot 196
Cooty McCootFace @cootymccootface.bsky.social · 13/12/2024Coot 1.1.11 Released o FEATURE: One can now dynamically edit SMILES in layla o FEATURE: Anisotropic atom representation [thanks to Global Phasing] o FEATURE: Electrostatic representation [Stuart McNicholas] o FEATURE: Function partition_map_by_chain() added and more. #coot 0128
Cooty McCootFace @cootymccootface.bsky.social · 12/12/2024Anisotropic representation of COD cif files in Coot 1.1.11 010
