 #!/bin/bash
 
 download_dir=/home/chuangkj/alphafold2_jax/downloads
 python3 run_alphafold.py \
 --fasta_paths=rcsb_pdb_8U23.fasta \
 --output_dir=./ \
 --use_precomputed_msas=false \
 --data_dir=$download_dir  \
 --uniref90_database_path=$download_dir/uniref90/uniref90.fasta \
 --mgnify_database_path=$download_dir/mgnify/mgy_clusters_2018_12.fa \
 --bfd_database_path=$download_dir/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
 --uniref30_database_path=$download_dir/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
 --pdb70_database_path=$download_dir/pdb70/pdb70 \
 --template_mmcif_dir=$download_dir/pdb_mmcif/mmcif_files \
 --obsolete_pdbs_path=$download_dir/pdb_mmcif/obsolete.dat \
 --max_template_date=2024-05-14 \
 --model_preset=monomer \
 --db_preset=full_dbs \
 --models_to_relax=best \
 --use_gpu_relax=false \
 --benchmark=true

 
 
 

