examples/alphafold3.md
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-# This is alphafold3 example
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+## AlphaFold3 Example
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+
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+### Download databases
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+
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+The databases for AlphaFOld3 (AF3) must be downloaded. We provide the script we used below. Adjust the DATABASE_DIR as needed.
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+
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+
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+```
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+#!/usr/bin/env bash
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+
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+## Alphafold 3.0.0 database download
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+## Pulled from provided fetch_databases.py
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+##
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+## JV Nov 21, 2024
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+## help@sbgrid.org
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+
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+# get zstd in path
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+export PATH=$PATH:$HOME/.local/bin
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+
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+files=(
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+ 'bfd-first_non_consensus_sequences.fasta.zst'
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+ 'mgy_clusters_2022_05.fa.zst'
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+ 'nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst'
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+ 'pdb_2022_09_28_mmcif_files.tar.zst'
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+ 'pdb_seqres_2022_09_28.fasta.zst'
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+ 'rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst'
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+ 'rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst'
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+ 'uniprot_all_2021_04.fa.zst'
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+ 'uniref90_2022_05.fa.zst'
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+)
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+
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+DATABASE_DIR="/programs/local/alphafold-3.0.0/databases"
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+GOOGLE_URL="https://storage.googleapis.com/alphafold-databases/v3.0"
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+
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+for filename in "${files[@]}"; do
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+ echo "Fetching: $filename"
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+ echo "curl --progress-bar --continue-at - --output ${DATABASE_DIR}/${filename} ${GOOGLE_URL}/${filename} "
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+done
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+
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+for filename in "${files[@]}"; do
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+ echo "Uncompressing: $filename"
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+ echo "zstd --decompress --force ${DATABASE_DIR}/${filename}"
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+done
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+
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+```
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+
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+
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+
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+The resulting layout:
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+
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+```
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+/programs//local/alphafold-3.0.0/databases/
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+├── bfd-first_non_consensus_sequences.fasta
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+├── compressed
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+│   ├── bfd-first_non_consensus_sequences.fasta.zst
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+│   ├── mgy_clusters_2022_05.fa.zst
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+│   ├── nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst
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+│   ├── pdb_2022_09_28_mmcif_files.tar.zst
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+│   ├── pdb_seqres_2022_09_28.fasta.zst
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+│   ├── rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst
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+│   ├── rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst
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+│   ├── uniprot_all_2021_04.fa.zst
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+│   └── uniref90_2022_05.fa.zst
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+├── mgy_clusters_2022_05.fa
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+├── nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta
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+├── pdb_2022_09_28_mmcif_files.tar
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+├── pdb_seqres_2022_09_28.fasta
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+├── rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta
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+├── rnacentral_active_seq_id_90_cov_80_linclust.fasta
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+├── uniprot_all_2021_04.fa
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+└── uniref90_2022_05.fa
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+```
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+
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+###
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+```