Running AlphaFold On Rivanna

Overall steps:

1. Prep the Working Environment

   • Install alphapickle and download the script for sequence coverage plot.

2. Get the Input

   • Get a FASTA file and put it on Rivanna via your preferred method (Globus, scp, etc).

3. Slurm Script

   • Create a SLURM script based on UVA RC AlphaFold documentation.
   • Include post-processing scripts at the end of the SLURM job (e.g., alphapickle) for sequence coverage plots and QC visualization.
   • This creates an all-in-one script that runs AlphaFold and visualizations in a single job.

4. Submit Job

   • Submit your slurm script using the command sbatch alphafold.slurm.

5. Visualize

   • Visualize QC plots and 3D structures in OOD Desktop.