examples/alphaflow.md
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-# AlphaFlow Example
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+## AlphaFlow Example
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+
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+In order to run AlphaFlow with SBGrid you must:
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+1. Obtain the alphaflow model weights
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+
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+2. Obtain MSAs for your sequences
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+These steps are included in the example script below. We use a test input csv file provided with AlphaFlow.
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+Edit the project_dir variable to point to your own project directory.
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+```
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+## AlphaFlow Example
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+## https://github.com/bjing2016/alphaflow
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+##
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+## help@sbgrid.org
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+## Dec 3, 2024
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+
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+
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+source /programs/sbgrid.shrc
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+export ALPHAFLOW_X=20241203_86d7606
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+
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+verdir=/programs//x86_64-linux//alphaflow/20241203_86d7606
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+project_dir=/build/source/alphaflow/20241203_86d7606
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+
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+cd ${project_dir}
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+
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+## Get weights
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+## AlphaFlow-PDB distilled
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+mkdir weights
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+wget -P ./weights https://storage.googleapis.com/alphaflow/params/alphaflow_pdb_distilled_202402.pt
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+
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+## Sample input file
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+## edit to contain just one sequence for testing
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+cp ${verdir}/alphaflow/splits/atlas_test.csv ./
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+
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+## Generate MSAs from colabfold
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+python.alphaflow ${verdir}/alphaflow/scripts/mmseqs_query.py --split ./atlas_test.csv --outdir ./msa
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+
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+## Run model
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+python.alphaflow ${verdir}/alphaflow/predict.py --mode alphafold --input_csv ${project_dir}/atlas_test.csv --msa_dir ${project_dir}/msa --weights ${project_dir}/weights/alphaflow_pdb_distilled_202402.pt --samples 1 --outpdb ${project_dir}/out_pdb
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+```