coot installation guide

[biotech70]

How can I install this tool in Ubuntu v22.04? What is the best COOT installation guide? And how to access it?

[pemsley]

Hello @biotech70 The preferred method at the moment is to run the script built-it-3-3 for Coot 1 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html If the build goes wrong we can discuss it here.

[biotech70]

This link's content has been checked. I can't find a clear user guide for installing Coot.

[YoshitakaMo]

If you can use Linuxbrew on your Ubuntu 22.04, you can install coot 1 in the same way as on a Mac.

brew install wget
wget https://raw.githubusercontent.com/YoshitakaMo/homebrew-bio/coot/Formula/coot.rb -O coot.rb
brew install ./coot.rb --verbose --debug --keep-tmp --HEAD

[pemsley]

Thank you @YoshitakaMo

[biotech70]

I try to do it but after many times and in the last step got this error.

[YoshitakaMo]

I forgot to mention that the error sometimes occurs when installing from scratch because it depends on a lot more packages than Homebrew/Linuxbrew usually assumes. Try again brew install ./coot.rb --verbose --debug --keep-tmp --HEAD and maybe the error will be passed.

[biotech70]

Thanks for your guide @YoshitakaMo

[Adwaith99]

Hi,

When I am trying to use the "build-it-3-3" scipt on ubuntu, it just fails with the following error as shown in the image.

[GuShaocheng]

Hello @biotech70 The preferred method at the moment is to run the script built-it-3-3 for Coot 1 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html If the build goes wrong we can discuss it here.

Hi, I followed this script and build the coot 1 on ubuntu22.04.

• During compiling, <pygobject-3.0/pygobject.h> is required from the system even though pygobject has been made in the first part of the script. Or it designs so that it should be installed manually.
• after finishing, if I run XX/bin/coot, I only can see a one-second GUI of coot, and coot crashes. But I can successfully run coot via XX/libexec/coot-bin.
• after launching coot 1, I can load pdb and mrc map. However, some functions seem to be missing. Most validation tools and some calculation tools don't work, such as the Ramachandran plot. And custom python scripts can't be executed.
• Lastly, I found when I forced nvidia GPU when running coot, coot said: No available configurations for the given RGBA pixel format. It would crash if loading pdb.

All the best!

[AndreTomasGraca]

If you can use Linuxbrew on your Ubuntu 22.04, you can install coot 1 in the same way as on a Mac.

brew install wget
wget https://raw.githubusercontent.com/YoshitakaMo/homebrew-bio/coot/Formula/coot.rb -O coot.rb
brew install ./coot.rb --verbose --debug --keep-tmp --HEAD

@YoshitakaMo, is this ready only to work on Ubuntu 22.04? I am trying to brew it on Ubuntu 20.04, but I get an error very similar to what is described here: https://github.com/brewsci/homebrew-bio/issues/1601

In my case it comes right after trying to install coot dependency gemmi

==> Installing coot dependency: brewsci/bio/gemmi
==> Pouring gemmi--0.5.6.x86_64_linux.bottle.tar.gz
/usr/bin/env tar --extract --no-same-owner --file /home/angr5008/.cache/Homebrew/downloads/ec23f99e9f74ba119ea9ef695eb425c8fb7d09a7c85b6c882bee6d555a5a2cd3--gemmi--0.5.6.x86_64_linux.bottle.tar.gz --directory /tmp/d20230614-880031-vlgf0y
/usr/bin/env cp -pR /tmp/d20230614-880031-vlgf0y/gemmi/. /home/linuxbrew/.linuxbrew/Cellar/gemmi
Error: cannot normalize PT_NOTE segment: non-contiguous SHT_NOTE sections

I have also tried to install the formula cootgtk4.rb and I hit exactly the same error.

Also, another clarification: using the coot.rb formula, which pre-release version of coot1 is being installed?

[YoshitakaMo]

I am a contributor to the homebrew-bio repository and created gemmi formula for this purpose, but the homebrew-bio repository is not active recently, so I can't fix this issue now...

[pemsley]

Also, another clarification: using the coot.rb formula, which pre-release version of coot1 is being installed?

HEAD is for Coot 1.06-pre. I really should make it a proper release. Maybe next week or so.

[jpspadeto2]

Hi, Paul!

I tried to open gtk4-demos and it opened normally. Yesterday, I ran ./build-it-3.3 as sudo and opened /autobuild/Linux-fedora-gtk4/bin/coot. It opened normally, but it doesn’t work with my regular user. I’m not sure if it’s related to permissions.