Af2 - #48
Af2#48
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ChristineSchulz
commented
Aug 28, 2026
ChristineSchulz
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- clear naming between AlphaFold 2 and 3
- AlphaFold 2 notebook and analysis notebook
- AlphaFold 2 tutorial
…b into molecular_dynamics
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iulusoy
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iulusoy
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Looks good to me! Overall the insulin run is quite long, and it can happen that you cannot finish this all in one hour, so if there is a way to loosen parameter constraints so that it runs faster; or take a smaller example, I think that would provide a better user experience.
I provided links and names to the notebook files, as well as a link to the fasta file which I had to search in the repo.
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "ALPHAFOLD_WORKING_DIR = Path.cwd() / \"alphafold2\"\n", |
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We were not instructed to create this subdirectory - either instruct so or use the same dir as the notebook is in
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Yes, make that more explicit in the tutorial.
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "ALPHAFOLD_WORKING_DIR = Path.cwd() / \"alphafold2\"\n", |
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without creating this output path, the run.sh will not work.
| "outputs": [], | ||
| "source": [ | ||
| "# working directory\n", | ||
| "ALPHAFOLD_WORKING_DIR = Path.cwd() / \"alphafold2\"\n", |
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Same here, either tell explicitly to construct exactly that subfolder in the new folder, or drop the subfolder
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