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Predicting a single protein structure using Alphafold on Notos

Setup

  1. Copy the alphafold folder from /mnt/beegfs/alphafold/alphafold to your home directory
    • When you log in to notos you are automatically in your home directory
    • Run the command below to copy the folder into your home directory
    • cp -r /mnt/beegfs/alphafold/alphafold/ .
    • This folder has all the required updates to run alphafold successfully
  2. Locate the folder named docker by running the command cd alphafold/docker
  3. Open run_docker.py by running the command vi run_docker.py
    • Press i to insert and make edits to the file
    • Change the destination folder output_dir on line 49 to a folder you wish the results are saved into
    • Make sure you have sufficient read and write permissions for the output_dir folder

Running Alphafold

  1. To run alphafold, go back to the home directory by running the command cd
  2. Type the command python3 ~/alphafold/docker/run_docker.py --fasta_paths=path_to_sequence --max_template_date=YYYY-MM-DD --data_dir=/mnt/beegfs/alphafold/databases
    • For example: python3 ~/alphafold/docker/run_docker.py --fasta_paths=T1050.fasta --max_template_date=2020-05-14 --data_dir=data_dir=/mnt/beegfs/alphafold/databases
    • For optimized performance use the preset reduced_dbs. For example: python3 ~/alphafold/docker/run_docker.py --fasta_paths=T1050.fasta --max_template_date=2020-05-14 --model_preset=monomer --db_preset=reduced_dbs --data_dir=data_dir=/mnt/beegfs/alphafold/databases
    • You can use the date variable for the max_template_date by running the command today = `date +%Y-%m-%d` and setting max_template_date to max_template_date = $today
  3. Other presets and options can be found here

Using a GNU screen

To be able to detach and disconnect from a process without interrupting the procedure use GNU screen sessions:

  1. Follow the setup process above
  2. To start a named screen session, type the following in your console screen -S session_name
  3. Run the required alphafold commands
  4. To detach from a linux screen session, press Ctrl+a d
  5. To get the list of current running sessions, type the following screen -ls
  6. To reattach to a linux screen, type the following screen -r session_name
  7. More on GNU screen sessions can be found here.

Site Last Updated: December 18, 2022