Rosettafold-All-Atom Example

Below we provide a sample bash script, a fasta file renamed from one of the RFAA examples and a config yaml file.

You must run RFAA outside of the installation directory.

In order to do this you must provide your own config yaml file(s) and set the location of this yaml file. We show an example using the --config-dir option from hydra.

These environment variables must be set:

ROSETTAFOLDAA_X

ROSETTAFOLD_DB_PATH

RFAA_DIR

DGLBACKEND

In addition, the script below uses a project directory that needs to be set or changed:

The example script expects two files in the current directory:

sbgrid_example.yaml 

and

sbgrid_example.fasta

We purposely renamed these example files to be sure we're using our own files and not the examples files that come with RFAA.

!/usr/bin/env bash

SBGrid RosettaFold-All-Atom example

help@sbgrid.org

May 13, 2024

SLURM

SBATCH --mem=64G

SBATCH -t 2:00:00

SBATCH -p gpu_quad

SBATCH --gres=gpu:1

MY_PROJ_DIR= cd ${MY_PROJ_DIR}

module load cuda/11.2

Start SBGrid environment

source /programs/sbgrid.shrc

Set version of RFAA

export ROSETTAFOLDAA_X=bf21483

Set critical env variables

export DGLBACKEND=pytorch export ROSETTAFOLD_DB_PATH=/n/shared_db/RoseTTAFold export RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${ROSETTAFOLDAA_X}/RoseTTAFold-All-Atom

Call the correct python bundled with RFAA

python.rfaa --version

Run inference, override hydra parameters from YAML file

python.rfaa -m rf2aa.run_inference \ --config-name sbgrid_example --config-dir ./ \ checkpoint_path=${RFAA_DIR}/RFAA_paper_weights.pt \ database_params.command=${RFAA_DIR}/make_msa.sh \ database_params.hhdb=${ROSETTAFOLD_DB_PATH}/pdb100_2021Mar03/pdb100_2021Mar03