diff --git a/README.md b/README.md index 0864122ca25bb514c215d128b744be07f8b9772b..415b2f26ec7df51c54d51499f5eaa8b2ec124fb8 100644 --- a/README.md +++ b/README.md @@ -73,6 +73,16 @@ python run_alphafold.py \ --output_dir=/root/af_output ``` +There are various flags that you can pass to the `run_alphafold.py` command, to +list them all run `python run_alphafold.py --help`. Two fundamental flags that +control which parts AlphaFold 3 will run are: + +* `--run_data_pipeline` (defaults to `true`): whether to run the data + pipeline, i.e. genetic and template search. This part is CPU-only, time + consuming and could be run on a machine without a GPU. +* `--run_inference` (defaults to `true`): whether to run the inference. This + part requires a GPU. + ## AlphaFold 3 Input See the [input documentation](docs/input.md).