examples/alphafold2.md
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@@ -33,25 +33,31 @@ These databases can be downloaded with the included download script and the aria
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The database directory shouuld look like this :
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```
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-├── bfd
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+.
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+├── bfd
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│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
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│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
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│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
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│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
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-│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
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+│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
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│   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
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├── mgnify
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-│   └── mgy_clusters.fa
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+│   ├── mgy_clusters_2018_12.fa
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├── params
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│   ├── LICENSE
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+│   ├── params_model_1_multimer.npz
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│   ├── params_model_1.npz
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│   ├── params_model_1_ptm.npz
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+│   ├── params_model_2_multimer.npz
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│   ├── params_model_2.npz
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│   ├── params_model_2_ptm.npz
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+│   ├── params_model_3_multimer.npz
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│   ├── params_model_3.npz
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│   ├── params_model_3_ptm.npz
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+│   ├── params_model_4_multimer.npz
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│   ├── params_model_4.npz
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│   ├── params_model_4_ptm.npz
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+│   ├── params_model_5_multimer.npz
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│   ├── params_model_5.npz
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│   └── params_model_5_ptm.npz
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├── pdb70
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@@ -66,14 +72,15 @@ The database directory shouuld look like this :
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│   └── pdb_filter.dat
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├── pdb_mmcif
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│   ├── mmcif_files
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-│   ├── obsolete.dat
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-│   └── raw
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+│   └── obsolete.dat
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+├── pdb_seqres
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+│   └── pdb_seqres.txt
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├── small_bfd
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│   └── bfd-first_non_consensus_sequences.fasta
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├── uniclust30
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│   └── uniclust30_2018_08
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-└── uniref90
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- └── uniref90.fasta
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+├── uniprot
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+│   └── uniprot.fasta
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```
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### Using the default run_alphafold.sh wrapper