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Created a new Markdown file to store the information from [https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshop1_PyMOL.pdf](https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshop1_PyMOL.pdf) and made updates and edits where necessary. I also added images to help illustrate the instructions that were given before the exercises.
Changed the `pyrosettacolabsetup` command in at the beginning of the notebooks to include the `cache_wheel_on_google_drive=False, serialization=False, mirror=0` options. Added back in the instructions for how to install a specific PyRosetta wheel in notebook 1.01.
lyskov
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Feb 12, 2026
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LGMT, - thank you for taking care of this @rclune ! Please see minor comment below. One more thing before we can merge this is that we need to update the student version of notebooks. Could you please run https://github.com/RosettaCommons/PyRosetta.notebooks/blob/master/make-student-nb.bash locally and commit the changes? (script should generate students version automatically, might be a good idea to do so inside Docker Python container)
Thanks,
| "1) Go to https://els.comotion.uw.edu/licenses/88 and fill out the form for a free academic license for PyRosetta\n", | ||
| "\n", | ||
| "2) Download PyRosetta correct PyRosetta-wheel (ie version that match your operation system and Python version) from https://www.pyrosetta.org/downloads and use your terminal to execute `pip install <downloaded-wheel>` ((you may need to add sudo before the `pip` part if your computer says you don’t have permission)\n", | ||
| "2) Download the latest quarterly release of PyRosetta via \n", |
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The wording here might be slightly off. Perhaps:
“Install the latest quarterly PyRosetta release by pointing pip to the wheel archive directory.”
| "source": [ | ||
| "!pip install pyrosettacolabsetup\n", | ||
| "import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n", | ||
| "import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta(cache_wheel_on_google_drive=False, serialization=False, mirror=0)\n", |
| "Analyze the energy between residues Y102 and Q408 in cetuximab (PDB code 1YY9, use the `pyrosetta.toolbox.pose_from_rcsb` function to download it and load it into a new `Pose` object) by following the steps below. \n", | ||
| "\n", | ||
| "A. Internally, a Pose object has a list of residues, numbered starting from 1. To find the residue numbers of Y102 of chain D and Q408 of chain A, use the residue chain identifier and the PDB residue number to convert to the pose numbering using the `pose2pdb()` method:\n", | ||
| "A. Internally, a Pose object has a list of residues, numbered starting from 1. To find the residue numbers of Y102 of chain D and Q408 of chain A, use the residue chain identifier and the PDB residue number to convert to the pose numbering using the `pdb2pose()` method:\n", |
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@lyskov I ran the script to create the student notebooks and updated the wording in notebook 01.01. |
colabxterm was causing issues with running the notebooks on the testing server, this change should fix it. PR link: [#619](RosettaCommons/rosetta#619 (review))
lyskov
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Feb 24, 2026
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In this PR I...
notebooksdirectory. I will add it to the TOC and/or make a new page for it on the PyRosetta website in the future.mirroroption and 1.01 to point to the quarterly releases instead of having users download wheels