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Cooty McCootFace @cootymccootface.bsky.social · 03/04/2026

Quick Demo of Agentic Coot www.youtube.com/watch?v=NkBA... (Yes, there is still work to do.)

youtube.com

Agentic Coot working with Claude

YouTube video by Paul Emsley

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Cooty McCootFace @cootymccootface.bsky.social · 03/04/2026

Coot 1.2 released With side-by-side stereo and Agentic Coot pemsley.github.io/coot/blog/20... pemsley.github.io/coot/blog/20...

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Cooty McCootFace @cootymccootface.bsky.social · 15/03/2026

You can now make attractive-looking, dynamic, interactive in-line graphs in Claude Desktop using Agentic Coot (HEAD, not release that is - for the moment)

Graph from Claude Desktop showing B-factor variation

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Cooty McCootFace @cootymccootface.bsky.social · 05/06/2025

Coot 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

An example carborane molecule represented in Coot - 6yzn

Coot with anisotropic atom probability turned up to 100% for 5vof

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Cooty McCootFace @cootymccootface.bsky.social · 01/04/2025

Coot 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

Imagen3 generated image - the prompt was something like "give me a cartoon coot with its claw reaching out and touching a cartoon representation of a protein" - I added the screenshot after that.

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Cooty McCootFace @cootymccootface.bsky.social · 17/03/2025

Coot 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

Screenshot of 2d ligand environment view, 1x8b 4dfr, 2vtq, 2p4y

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Cooty McCootFace @cootymccootface.bsky.social · 15/03/2025

Human 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!

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Cooty McCootFace @cootymccootface.bsky.social · 14/03/2025

Solid-modelled symmetry atoms, so that you can see symmetry on macOS. Before and after Coot 1.1.14 coming soon! # coot

Difficult to see symmetry atoms on macOS Coot 1.1 screenshot

Easy to see symmetry atoms on macOS Coot 1.1 screenshot

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Cooty McCootFace @cootymccootface.bsky.social · 08/03/2025

Alphafold PAE plot added to Coot 1! Coot 1.1.14 coming soon! #coot

Coot screenshot alphafold model for Q8W3K0 including PAE figure

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Cooty McCootFace @cootymccootface.bsky.social · 02/03/2025

You can represent atom selections as Metaballs in Moorhen Models → + → Style → Metaballs #moorhen

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Cooty McCootFace @cootymccootface.bsky.social · 24/02/2025

Coot 1.1.13 Released SSM Superpose works! NCS Ghosts works! CA label tracking on "spacing" through chain! #coot

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Cooty McCootFace @cootymccootface.bsky.social · 20/02/2025

After years of (off and on) effort, Coot 1 finally compiles and runs on Alma Linux!

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Cooty McCootFace @cootymccootface.bsky.social · 12/02/2025

Coot 1.1.12 Released: Graphics viewport scaling, Acedrg Link, HOLE and several fixes pemsley.github.io/coot/blog/20...

pemsley.github.io

Release 1.1.12

Release 1.1.12 o source tar:

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Cooty McCootFace @cootymccootface.bsky.social · 07/02/2025

HOLE-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

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Cooty McCootFace @cootymccootface.bsky.social · 05/02/2025

Coot's Ligand Builder now has dark-mode icons and dynamic QED scoring... 1.1.12 out soon! #coot

Coot Layla screenshot with QED and dark-mode icons

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Cooty McCootFace @cootymccootface.bsky.social · 01/02/2025

Moorhen 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!

Screenshot of moorhen.org in gallery mode.

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Cooty McCootFace @cootymccootface.bsky.social · 26/01/2025

Quiz 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?

Screenshot of LLP and environment with electron density from 1ajs

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Cooty McCootFace @cootymccootface.bsky.social · 25/01/2025

Coot's new Acedrg Link interface Coot 1.1.12 out soon! #coot

Coot Screenshot with Acedrg Link overlay dialog

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Cooty McCootFace @cootymccootface.bsky.social · 25/01/2025

Coot 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

Coot screenshot failing to refine a ligand

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Cooty McCootFace @cootymccootface.bsky.social · 17/01/2025

After looking at EM maps for months, the Holton "Untangle Challenge" map looks so pretty...

Protein model 1aho and electron density shown in Coot

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Cooty McCootFace @cootymccootface.bsky.social · 16/01/2025

A few slides from Lucrezia Catapano's recent CCP4 Study Weekend presentation - there will be a CCP4 YouTube video at some stage

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Cooty McCootFace @cootymccootface.bsky.social · 10/01/2025

Lucrezia Catapano has a style all her own when giving a Coot presentation...

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Cooty McCootFace @cootymccootface.bsky.social · 13/12/2024

Coot has a built-in Poisson–Boltzmann solver and can make electrostatic surfaces quite snapily these days (8r96 in this example) #coot

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Cooty McCootFace @cootymccootface.bsky.social · 13/12/2024

Coot 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

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Cooty McCootFace @cootymccootface.bsky.social · 12/12/2024

Anisotropic representation of COD cif files in Coot 1.1.11

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