Luca Jovine

You could try OpenFold (https://github.com/aqlaboratory/openfold) with the described tweaks to minimize memory usage...

> Update > After I recreated the docker image, the changed variables were applied. I confirm that this indeed does the job. After: ``` perl -p -i -e 's/n_cpu: int...

@ericmjl absolutely! Ideally one would want something builtin, which - considering that one cannot split a single prediction over multiple GPUs - could be something like the following: ``` import...

No, sorry, I meant multiple-model inference (I also got confused as we often use the term ensembles for MR model sets). But how does one then tell OF how many...

Sorry, I think I did not explain myself well. By models I meant output PDB models, i.e. the equivalent of "ranked_0.pdb... ranked_4.pdb" of AF2 (monomer).

Thanks for the explanation, it's nice that one can also generate PDBs with AF2 and OF models at the same time (based on 'Exactly one of --openfold_checkpoint_path or --jax_param_path must...

Great, thank you!

I also cannot see the attachments due to a 404 error. For example: ``` > slack-export-viewer -z test Archive already extracted. Viewing from /Users/luca/test... WARNING: This is a development server....

Sure, of course. This was my input FASTA: ``` >protein1 IDWDVYCSQDESIPAKFISRLVTSKDQALEKTEINCSNGLVPITQEFGINMMLIQYTRNELLDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPK >protein2 RSWHYVEPKFLNKAFEVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTHWANYMLWINKKIDALGRTPVVGDYTRLGAEIGRRIDMAYFYDFLKDKNMIPKYLPYMEEINRMRPADVPVKYM ``` (which basically corresponds to our PDB deposition 5IIB) Flags were --db_preset=full_dbs --model_preset=multimer --num_multimer_predictions_per_model=1 --gpu_devices="0" --max_template_date=3000-01-01

Also... ``` > python run_alphafold.py --helpshort /usr/local/conda/miniconda3/envs/af2/lib/python3.7/site-packages/haiku/_src/data_structures.py:37: FutureWarning: jax.tree_structure is deprecated, and will be removed in a future release. Use jax.tree_util.tree_structure instead. PyTreeDef = type(jax.tree_structure(None)) Traceback (most recent call last):...