Cooty McCootFace

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!

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

Coot screenshot showing HOLE in 2y5m

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

Quantifying the chemical beauty of drugs Druglikeness 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...

QED: Quantifying the chemical beauty of drugs:
pmc.ncbi.nlm.nih.gov/articles/PMC...

(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.

Coot Layla screenshot with QED and dark-mode icons

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

Ugh.

Screenshot of moorhen.org in gallery mode.

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!

Distance 2.6Å.

Screenshot of LLP and environment with electron density from 1ajs

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?

Coot Screenshot with Acedrg Link overlay dialog

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

Coot screenshot failing to refine a ligand

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