Oops. Thanks. Fixed now.

Agentic Coot working with Claude YouTube video by Paul Emsley

Quick Demo of Agentic Coot

www.youtube.com/watch?v=NkBA...

(Yes, there is still work to do.)

This is the correct Release Notes for 1.2
pemsley.github.io/coot/blog/20...

Side-by-side ribbon diagram in coot.

Coot 1.2 released

With side-by-side stereo

and Agentic Coot

pemsley.github.io/coot/blog/20...

pemsley.github.io/coot/blog/20...

These look beautiful.

This is cool. A hover-over popup with the chemical diagram would also be cool. I'll see what I can do.

FYI to the public (not to Oli): the visual effect is more clean and impactful that it seems given this video compression.

Not yet. I need to teach it about servalcat and ligand fitting.

Note 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).

Well... 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.

Graph from Claude Desktop showing B-factor variation

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)

An example carborane molecule represented in Coot - 6yzn

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

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

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.

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

Is the symmetry problem related to you Github question?

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

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

Just to be clear, I mean this image is freely reproducible - not the Science paper!

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!

Difficult to see symmetry atoms on macOS Coot 1.1 screenshot

Easy to see symmetry atoms on macOS Coot 1.1 screenshot

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

Have a Cigar?

Old Coot is still Good Coot! Haha!

Me too.

You'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.

Coot-1 lives in the "coot_py3" directory in a CCP4 distribution.

Coot screenshot alphafold model for Q8W3K0 including PAE figure

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

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

Github notification that homebrew bottles have been updated.

Coot from Homebrew has been updated!
Yay Yoshitaka Moriwaki!

There's still lots of (very dull) work for us to do before we can robustly write modern mmCIF.

Welcome to the party!

Coot screenshot showing NCS ghosts

Coot 1.1.13 Released

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

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