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Update alphafold.md
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lauraluebbert committed Mar 7, 2024
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Expand Up @@ -4,8 +4,11 @@ Predict the 3D structure of a protein from its amino acid sequence using a simpl
Returns: Predicted structure (PDB) and alignment error (json).

Before using `gget alphafold` for the first time:
1. Install the third-party dependency openmm v7.5.1 (or v7.7.0 for Python >= 3.10) by running the following command from the command line: `conda install -qy conda==4.13.0 && conda install -qy -c conda-forge openmm=7.5.1` (or `openmm=7.7.0` for Python >= 3.10). (Recommendation: Follow with `conda update -qy conda` to update conda to the latest version afterwards.)
2. Run `gget setup alphafold` / `gget.setup("alphafold")` once (also see [`gget setup`](setup.md)). Running `gget setup alphafold` / `gget.setup("alphafold")` will download and install the latest version of AlphaFold2 hosted on the [AlphaFold GitHub Repo](https://github.com/deepmind/alphafold). You can rerun this command any time to update the software after a new AlphaFold release.
1. Install the third-party dependency openmm v7.5.1 (or v7.7.0 for Python >= 3.10) by running the following command from the command line:
`conda install -qy conda==4.13.0 && conda install -qy -c conda-forge openmm=7.5.1`
(replace with `openmm=7.7.0` for Python >= 3.10)
Recommendation: Follow with `conda update -qy conda` to update conda to the latest version afterwards.
3. Run `gget setup alphafold` / `gget.setup("alphafold")` once (also see [`gget setup`](setup.md)). Running `gget setup alphafold` / `gget.setup("alphafold")` will download and install the latest version of AlphaFold2 hosted on the [AlphaFold GitHub Repo](https://github.com/deepmind/alphafold). You can rerun this command any time to update the software after a new AlphaFold release.

**Positional argument**
`sequence`
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