On 26/01/2026 06:55, 刘红杰 wrote:
Dear Dr. Emsley,
My name is Liu Hongjie,
Hello Liu Hongjie,
an Assistant Researcher at the Capital Medical Innovation Center. I am
writing to seek your professional advice regarding Coot installation
and compatibility issues on my working environment, Ubuntu 24.04.3 LTS.
Key Issues I Encountered:
1. Library Installation Challenges On Ubuntu 24.04.3 LTS, I have
encountered difficulties installing the required system libraries for
Coot, particularly GTK2/GTK3-related dependencies. I previously
attempted to use Coot 1.1.19 (a GTK2-based version), but failed to
launch it due to missing GTK2 libraries—these legacy libraries are
either unavailable in the official repositories of Ubuntu 24.04.3 LTS
or have compatibility conflicts with the system’s default packages.
This is confused.
I don't have time to discuss installation issues from a version of Coot
from 6 years ago.
I am happy to discuss the 1.1.x series, e.g. 1.1.19 or 1.1.20. That is
based on GTK4.
2. Optimal Coot Version for Ubuntu 24.04.3 LTS I am uncertain which
Coot version is the most stable and recommended for Ubuntu 24.04.3
LTS. I noticed there is an experimental GTK4-based version of Coot
1.1, but I am concerned about its reliability for production work—my
primary use case is manual model building and refinement for cryo-EM
density maps (output from CryoSPARC and Phenix workflows).
I would say that the optimal version of Coot at the moment is 1.1.20.
I noticed there is an experimental GTK4-based version of Coot 1.1
Not as far as I know.
my primary use case is manual model building and refinement for cryo-EM density
maps (output from CryoSPARC and Phenix workflows).
Manual model building is done with a screwdriver and a pair of pliers.
Nobody does that anymore.
Coot is an interactive model-building program.
Anyway, Coot 1.1.x should work with Phenix and CryoSPARC output.
3. Alternative Installation Methods (Conda/Docker) I wonder if there
are official or community-supported methods to install Coot via Conda
(Anaconda/Miniconda) or Docker containers. These approaches would
effectively avoid system library conflicts, which is critical for
maintaining the stability of my working environment.
Yes, I think so, conda at least. Billy Poon was working on it - so you
may get the latest new on that by asking the Phenix mailing list.
Could you kindly provide guidance on the optimal Coot version for
Ubuntu 24.04.3 LTS,
why not just get it from the operating system, like you would anything else?
sudo apt update
sudo apt install coot
Or you could get it from Flatpak (Ubuntu is not the environment where
Flatpak is most at home, so you will have to do a bit of work to sort
out the installation).
Paul.
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