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ChristineSchulz
commented
Feb 2, 2026
ChristineSchulz
commented
- added notebooks / tutorial / pytest for bindcraft, boltz, boltzgen, RFDiffusion on bwVisu
- adapted website for longer content in the tutorials
- adapted other website pages accordingly
- added cute favicon
Added module loading and conda activation commands to run.sh
Removed a code cell that checks the location of the 'boltzgen' executable.
This reverts commit d9ba101.
…eHub into origin/protein_design
fighting macOS random failures
…eHub into origin/protein_design
Disabling macOS until I figure out what happens there
…eHub into origin/protein_design
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iulusoy
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iulusoy
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I like the re-structuring of the resources and the new tutorials.
So far, I have only reviewed the bindcraft one, but am already submitting the comments thus far.
I have no idea why and when I should use bindcraft, and what all the output files are. Maybe it could be useful to add one or two sentences about this. Other than that, the tutorial worked very smoothly.
| To use Bindcraft, we need to request a GPU core of type A40. | ||
| Choose the Kernel Path to Bindcraft: `/mnt/sds-hd/sd25g005/bindcraft/share/jupyter/` [Contact us](/contact.md) for access to this shared directory. | ||
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I understand that you do not want to place images for each tutorial for this in the repo, but I think some users may miss the point about the kernel path. So I would at least also mark the kernel path with a red square, if not put the correct path in the box and take another screenshot.
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I think you already changed this in the meantime, so please disregard the comment.
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| ### Step 2: Connect to bwVisu and Start Jupyter | ||
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| Go to [https://bwvisu.bwservices.uni-heidelberg.de/](https://bwvisu.bwservices.uni-heidelberg.de/ ) and log in with your credentials and one-time password. Please note that you need to be connected to Heidelberg University's VPN if you are connecting from outside the campus. |
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The link opens in the same tab when using markdown syntax. You could also consider using html for the link and then force it to open in a new tab, for better user experience. I am not sure if this would apply to any other link.
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| In the notebook you can check the modules by checking the output of `! module list` which should look like that: |
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Step 4 Open the notebook
Then check the modules and imports
Start the calculation is then Step 5
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| "source": [ | ||
| "BINDCRAFT_WORKING_DIR = Path.home() / \"protein_design_w_Bindcraft\"" |
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| "BINDCRAFT_WORKING_DIR = Path.home() / \"protein_design_w_Bindcraft\"" | |
| "BINDCRAFT_WORKING_DIR = Path.cwd() |
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Because otherwise everyone has to place it in exactly the same folder in home, which I did not do and of course creates issues. Even if you tell people to do it this way, they will not for some reason and then get stuck.
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Why is the pre-commit hook |
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