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Fixes for steered MD tutorial and update to RBFE tutorial #33

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@mb2055 mb2055 commented Feb 21, 2025

This brings the tutorials in line with the latest version of BioSimSpace.
Changes are in two places:

  1. 04_FEP/02_RBFE - Now able to use the latest version of Cinnabar (also retains support for older versions). @annamherz I wasn't sure if there was a specific reason why cinnabar 0.3.0 was the one used, so I made sure the notebook still supports this version, but also later versions.
  2. 03_steered_md - There had been some changes to the API and the tutorial was out of date. @lohedges I wasn't completely sure about the best choices for align_selection and rmsd_selection so I chose the same region for both, if there's a better choice here its easy to change.

@mb2055 mb2055 requested a review from lohedges February 21, 2025 16:13
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  1. 4_FEP/02_RBFE - Now able to use the latest version of Cinnabar (also retains support for older versions). @annamherz I wasn't sure if there was a specific reason why cinnabar 0.3.0 was the one used, so I made sure the notebook still supports this version, but also later versions.

Hi! From what I recall, there wasn't a specific reason, mainly that the analysis was stable with that version at the time of writing 😄

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Just to note that the updated steered molecular dynamics tutorial requires an update to an input file within the data archive. Since these aren't versioned, I suggest creating a new archive on SharePoint, e..g data2.tar.bz2, then downloading it to the same archive name within the download script, i.e. data.tar.bz2. That way we don't break backwards compatibility for old versions of the tutorial.

@jmichel80: This file needs to replace reference.pdb in the data.tar.bz2 archive. The SharePoint link appears to be from your account, so it would probably be easiest if edit this. I suggest doing:

  1. Download and upack the archive.
  2. Replace the reference.pdb file with the one posted here.
  3. Create a new archive call data2.tar.bz2 (or give it a more meaningful name if you want to version it according to year, etc) and upload.
  4. Create a download link for the new archive and update in the get_tutorials.py file. (I can do this if needed. You'd just need to share the link.)

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