From dd913f0a28030c672bd3b841fefc8969a3d8eac6 Mon Sep 17 00:00:00 2001 From: "Laura Luebbert, Ph.D." <56094636+lauraluebbert@users.noreply.github.com> Date: Thu, 23 Jan 2025 16:10:45 -0500 Subject: [PATCH] Update alphafold.md --- docs/src/en/alphafold.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/docs/src/en/alphafold.md b/docs/src/en/alphafold.md index ed892b92..d045ff0a 100644 --- a/docs/src/en/alphafold.md +++ b/docs/src/en/alphafold.md @@ -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**