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Cooty McCootFace @cootymccootface.bsky.social · Jun 5

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 · Apr 1

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 · Mar 19

Is the symmetry problem related to you Github question?

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Cooty McCootFace @cootymccootface.bsky.social · Mar 17

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 · Mar 15

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

Cooty McCootFace @cootymccootface.bsky.social · Mar 15

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 · Mar 14

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 · Mar 14

Have a Cigar?

Cooty McCootFace @cootymccootface.bsky.social · Mar 14

Old Coot is still Good Coot! Haha!

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Cooty McCootFace @cootymccootface.bsky.social · Mar 10

Me too.

Cooty McCootFace @cootymccootface.bsky.social · Mar 9

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.

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Cooty McCootFace @cootymccootface.bsky.social · Mar 9

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

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Cooty McCootFace @cootymccootface.bsky.social · Mar 8

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 · Mar 2

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

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Cooty McCootFace @cootymccootface.bsky.social · Feb 25

Coot from Homebrew has been updated!
Yay Yoshitaka Moriwaki!

Github notification that homebrew bottles have been updated.

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Cooty McCootFace @cootymccootface.bsky.social · Feb 25

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

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Cooty McCootFace @cootymccootface.bsky.social · Feb 25

Welcome to the party!

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Cooty McCootFace @cootymccootface.bsky.social · Feb 24

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 · Feb 20

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 · Feb 12

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

Release 1.1.12

Release 1.1.12 o source tar:

pemsley.github.io

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Cooty McCootFace @cootymccootface.bsky.social · Feb 7

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 · Feb 6

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

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...

pmc.ncbi.nlm.nih.gov

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Cooty McCootFace @cootymccootface.bsky.social · Feb 6

(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.

Cooty McCootFace @cootymccootface.bsky.social · Feb 5

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 · Feb 4

Ugh.