1d69bd29ac4a4e13951633321060bddcb9463745
examples/alphafold2.md
... | ... | @@ -33,25 +33,31 @@ These databases can be downloaded with the included download script and the aria |
33 | 33 | The database directory shouuld look like this : |
34 | 34 | |
35 | 35 | ``` |
36 | -├── bfd |
|
36 | +. |
|
37 | +├── bfd |
|
37 | 38 | │ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata |
38 | 39 | │ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex |
39 | 40 | │ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata |
40 | 41 | │ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex |
41 | -│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata |
|
42 | +│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata |
|
42 | 43 | │ └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex |
43 | 44 | ├── mgnify |
44 | -│ └── mgy_clusters.fa |
|
45 | +│ ├── mgy_clusters_2018_12.fa |
|
45 | 46 | ├── params |
46 | 47 | │ ├── LICENSE |
48 | +│ ├── params_model_1_multimer.npz |
|
47 | 49 | │ ├── params_model_1.npz |
48 | 50 | │ ├── params_model_1_ptm.npz |
51 | +│ ├── params_model_2_multimer.npz |
|
49 | 52 | │ ├── params_model_2.npz |
50 | 53 | │ ├── params_model_2_ptm.npz |
54 | +│ ├── params_model_3_multimer.npz |
|
51 | 55 | │ ├── params_model_3.npz |
52 | 56 | │ ├── params_model_3_ptm.npz |
57 | +│ ├── params_model_4_multimer.npz |
|
53 | 58 | │ ├── params_model_4.npz |
54 | 59 | │ ├── params_model_4_ptm.npz |
60 | +│ ├── params_model_5_multimer.npz |
|
55 | 61 | │ ├── params_model_5.npz |
56 | 62 | │ └── params_model_5_ptm.npz |
57 | 63 | ├── pdb70 |
... | ... | @@ -66,14 +72,15 @@ The database directory shouuld look like this : |
66 | 72 | │ └── pdb_filter.dat |
67 | 73 | ├── pdb_mmcif |
68 | 74 | │ ├── mmcif_files |
69 | -│ ├── obsolete.dat |
|
70 | -│ └── raw |
|
75 | +│ └── obsolete.dat |
|
76 | +├── pdb_seqres |
|
77 | +│ └── pdb_seqres.txt |
|
71 | 78 | ├── small_bfd |
72 | 79 | │ └── bfd-first_non_consensus_sequences.fasta |
73 | 80 | ├── uniclust30 |
74 | 81 | │ └── uniclust30_2018_08 |
75 | -└── uniref90 |
|
76 | - └── uniref90.fasta |
|
82 | +├── uniprot |
|
83 | +│ └── uniprot.fasta |
|
77 | 84 | ``` |
78 | 85 | |
79 | 86 | ### Using the default run_alphafold.sh wrapper |