df99b4ed66716fd04648b64860407f6e2b1cd51b
examples/alphafold2.md
... | ... | @@ -145,6 +145,35 @@ Some command line flags have changed since version 2.0.0. We recommend running t |
145 | 145 | |
146 | 146 | |
147 | 147 | ### Examples |
148 | + |
|
149 | +**Alphafold2 2.3.1** |
|
150 | +``` |
|
151 | +/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \ |
|
152 | + --data_dir=/programs/local/alphafold/ \ |
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153 | + --output_dir=$(pwd) \ |
|
154 | + --fasta_paths=${input} \ |
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155 | + --max_template_date=2020-05-14 \ |
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156 | + --db_preset=full_dbs \ |
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157 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
158 | + --uniref30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
159 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
160 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
161 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
162 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
|
163 | + --use_gpu_relax=True \ |
|
164 | + --model_preset=monomer \ |
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165 | + --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 |
|
166 | +``` |
|
167 | + |
|
168 | +where the input fasta is |
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169 | + |
|
170 | +``` |
|
171 | +>T1083 |
|
172 | +GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED |
|
173 | +``` |
|
174 | + |
|
175 | +This is very similar to earlier 2.2.x releases, but the `--unicluster30_database_path` has been renamed to ` --uniref30_database_path`. |
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176 | + |
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148 | 177 | **NOTE : Alphafold2 introduced new flags for GPU-based relaxation that must be specifed**. |
149 | 178 | You can also resume from a previously run MSA. See [the alphafold2 github repo](https://github.com/deepmind/alphafold/releases/tag/v2.1.2) for more info. |
150 | 179 |