Skip to content

Commit

Permalink
Update alphafold.md
Browse files Browse the repository at this point in the history
  • Loading branch information
lauraluebbert authored Jan 23, 2025
1 parent c52531d commit dd913f0
Showing 1 changed file with 9 additions and 3 deletions.
12 changes: 9 additions & 3 deletions docs/src/en/alphafold.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,16 @@ 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:
1. Install the third-party dependency openmm by running the following command from the command line:
For Python versions < 3.10:
`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.
For Python version 3.10:
`conda install -qy conda==24.1.2 && conda install -qy -c conda-forge openmm=7.7.0`
For Python version 3.11:
`conda install -qy conda==24.11.1 && conda install -qy -c conda-forge openmm=8.0.0`

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**
Expand Down

0 comments on commit dd913f0

Please sign in to comment.