8ed877850b8ec83d30b8d8a68725895895cab8bf
examples/alphafold2.md
... | ... | @@ -143,8 +143,8 @@ Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`, |
143 | 143 | ``` |
144 | 144 | /programs/x86_64-linux/alphafold/2.1.2/bin.capsules/run_alphafold.py \ |
145 | 145 | --data_dir=/programs/local/alphafold/ \ |
146 | - --output_dir=/zpool_haumea/data/key/alphafold/test1 \ |
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147 | - --fasta_paths=200.fasta \ |
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146 | + --output_dir=$(pwd) \ |
|
147 | + --fasta_paths=${input} \ |
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148 | 148 | --max_template_date=2020-05-14 \ |
149 | 149 | --db_preset=full_dbs \ |
150 | 150 | --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
... | ... | @@ -153,10 +153,9 @@ Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`, |
153 | 153 | --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
154 | 154 | --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
155 | 155 | --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
156 | - --model_preset=multimer \ |
|
157 | 156 | --use_gpu_relax=True \ |
158 | - --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
|
159 | - --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta |
|
157 | + --model_preset=monomer \ |
|
158 | + --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 |
|
160 | 159 | ``` |
161 | 160 | |
162 | 161 | where test_monomer.fasta is |