alphafold
Here is an easy way to install alphafold2 on OSX in about 20 minutes and 7 easy steps. Based on the instructions here:
I’ve added a few fixes for dependencies (i.e. kalign and mmseqs2), permissions changes, combining installs, and corrections to the paths for newer systems.
I recommend you install anaconda navigator to get the base python packages and help making a root environment, you can do this on the command line, but I find the GUI easier to manage so you don’t end up in package hell! This prevents the need for complex dockers, containers, and environments:
https://www.anaconda.com/products/navigator
Enter these on your command line in order, and you should be up and running quickly:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install wget cmake gnu-sed brewsci/bio/hh-suite kalign mmseqs2 --cask miniforge
mkdir /Users/dellboy/Alphafold
cd /Users/dellboy/Alphafold
wget https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/install_colabbatch_M1mac.sh
chmod 777 ./install_colabbatch_M1mac.sh
bash ./install_colabbatch_M1mac.sh
When the installs are finished copy your fasta file into /Users/dellboy/Alphafold, for example:
https://rest.uniprot.org/uniprotkb/P13725.fasta (my first experimental structure!).
Then run the following command from your prompt, assuming you are still in /Users/dellboy/Alphafold directory.
./localcolabfold/colabfold-conda/bin/colabfold_batch --amber --templates --num-recycle 3 --model-order 1,2,3,4,5 ./P13725.fasta FFA2output
This run took just over 1 hour on my Mac Studio M2 Ultra.