examples/alphafold2.md
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@@ -143,8 +143,8 @@ Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`,
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```
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/programs/x86_64-linux/alphafold/2.1.2/bin.capsules/run_alphafold.py \
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--data_dir=/programs/local/alphafold/ \
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- --output_dir=/zpool_haumea/data/key/alphafold/test1 \
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- --fasta_paths=200.fasta \
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+ --output_dir=$(pwd) \
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+ --fasta_paths=${input} \
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--max_template_date=2020-05-14 \
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--db_preset=full_dbs \
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--bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
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@@ -153,10 +153,9 @@ Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`,
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--mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \
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--template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \
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--obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \
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- --model_preset=multimer \
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--use_gpu_relax=True \
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- --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \
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- --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta
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+ --model_preset=monomer \
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+ --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70
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```
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where test_monomer.fasta is