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Merge pull request #652 from lbarraga/alphafold-typos
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typo fixes in alphafold md
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boegel authored Aug 19, 2024
2 parents 1dc7d68 + 72c68e5 commit 0b26872
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8 changes: 4 additions & 4 deletions mkdocs/docs/HPC/alphafold.md
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Expand Up @@ -96,9 +96,9 @@ export ALPHAFOLD_DATA_DIR={{directory}}/{{version}}

### Running AlphaFold

AlphaFold provides run script called [run_alphafold.py](https://raw.githubusercontent.com/deepmind/alphafold/main/run_alphafold.py)
AlphaFold provides a script called [run_alphafold.py](https://raw.githubusercontent.com/deepmind/alphafold/main/run_alphafold.py)

A symbolic link named *alphafold* that points to the this script is included,
A symbolic link named *alphafold* that points to this script is included,
so you can just use `alphafold` instead of `run_alphafold.py` or `python run_alphafold.py` after loading the AlphaFold module.

The `run_alphafold.py` script has also been slightly modified such that defining the `$ALPHAFOLD_DATA_DIR` (see [above](./#setting-up-the-environment)) is sufficient to pick up all the data provided in that location,
Expand Down Expand Up @@ -158,7 +158,7 @@ This highlights the difference between CPU and GPU performance even more.
The following example comes from the official [Examples section]({{readme}}#examples) in the Alphafold [README]({{readme}}).
The run command is slightly different (see above: [Running AlphaFold](./running-alphafold)).

Do not forget to setup the environment (see above: [Setting up the environment](./setting-up-the-environment)).
Do not forget to set up the environment (see above: [Setting up the environment](./setting-up-the-environment)).

### Folding a monomer

Expand Down Expand Up @@ -193,7 +193,7 @@ The main difference between using a GPU or CPU in a job script is what module to
For running AlphaFold on GPU, use an AlphaFold module that mentions `CUDA` (or `cuda`),
for example `AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0`.

To run the jobs cripts you need to create a file named `T1050.fasta` with the following content:
To run the job scripts you need to create a file named `T1050.fasta` with the following content:

```fasta
>T1050 A7LXT1, Bacteroides Ovatus, 779 residues|
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