examples/alphafold3.md
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@@ -52,5 +52,73 @@ The resulting layout should look like this:
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└── uniref90_2022_05.fa
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```
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-###
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+### Run AlphaFold
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+
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+The script below provides a minimal example. You must provide the location of the model file.
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+
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+Edit PROJECT_DIR, MODEL_DIR and DATABASE_DIR as needed.
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+
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+We use the input json file given in the AF3 github readme; alphafold_input.json.
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+
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```
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+#!/usr/bin/env bash
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+
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+#SBATCH --partition=bch-gpu
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+#SBATCH --gres=gpu:large:1
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+#SBATCH --mem-per-cpu=24G
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+#SBATCH --time=04:00:00
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+#SBATCH --job-name=JV-AF3
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+
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+nvidia-smi --query-gpu=name,memory.total --format=csv
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+
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+## AlphaFold 3.0.0 example
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+## https://github.com/google-deepmind/alphafold3
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+##
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+## help@sbgrid.org
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+## Nov 11, 2024
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+
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+## Start SBGrid environment
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+source /programs/biogrids.shrc
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+export ALPHAFOLD_X=3.0.0
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+
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+export XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
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+# Memory settings used for folding up to 5,120 tokens on A100 80 GB.
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+export XLA_PYTHON_CLIENT_PREALLOCATE=true
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+export XLA_CLIENT_MEM_FRACTION=0.95
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+
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+PROJECT_DIR=/temp_work/ch199734/121503_alphafold3_3.0.0
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+MODEL_DIR=/home/ch199734/models
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+DATABASE_DIR=/programs/local/biogrids/alphafold-3.0.0/databases
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+
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+cd ${PROJECT_DIR}
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+
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+input_json=${PROJECT_DIR}/alphafold_input.json
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+
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+time run_alphafold.py \
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+ --json_path=${input_json} \
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+ --output_dir=${PROJECT_DIR}/af3_example_output \
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+ --db_dir=${DATABASE_DIR} \
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+ --model_dir=${MODEL_DIR}
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+
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+
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+```
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+
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+### [alphafold_input.json](https://github.com/google-deepmind/alphafold3)
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+
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+```
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+{
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+ "name": "2PV7",
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+ "sequences": [
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+ {
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+ "protein": {
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+ "id": ["A", "B"],
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+ "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG"
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+ }
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+ }
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+ ],
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+ "modelSeeds": [1],
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+ "dialect": "alphafold3",
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+ "version": 1
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+}
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+```
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+