Markdown format, PATH errors, internal link issue, python 2 issue, and suggestions

[jsgro]

• Reference 1: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial
• Reference 2: https://github.com/RosettaCommons/demos/blob/main/tutorials/ligand_docking/ligand_docking_tutorial.md

Format problem:
A Biochem student asked me for help to run the ligand docking (Reference 1 version) which has a break in the Markdown formatting just after the section labeled 3.2.4.. However, I see that on Reference 2 on github the format problem does not exist and might be caused by the server side of the rosettacommons.org https server (?)

PATH error:
There is one small PATH error in section 3.2.3.: when calling script molfile_to_params.py we are already within ligand_prep/ per instruction in section 3.1. Therefore the directory name should be removed from the last argument, keeping only eticlopride_conformers.sdf.

internal link issue:
At section 3.Next the link at the end of the line: "ligand preparation tutroial" has a typo, but on Reference 1 page goes the edit/create mode on a "Wiki" and gives error: "Forbidden. This wiki is set to no-edit mode." I found a suitable version as:
https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial

In the same way, the link called " [[RosettaScripts|rosetta_scripting]]" in Reference 2 causes the same no-edit mode error. I found what I believe to be a suitable replacement:
https://new.rosettacommons.org/demos/latest/tutorials/scripting_with_rosettascripts/scripting_with_rosettascripts

Python 2 issue:
The script calculate_ligand_rmsd.py on lines 83 and 221 use the print statement of Python version 2 and will cause an error. They need to be replaced with the "print function print(). I got help from Copilot to find a scriptable solution with sed:

# Assumes we are still in out directory
sed -r 's/^(\s*print)\s+(.*)/\1(\2)/g' ../scripts/calculate_ligand_rmsd.py > ../scripts/calculate_ligand_rmsd.py3
# make it executable
chmod a+x ../scripts/calculate_ligand_rmsd.py3

Note: sed -r -i to overwrite the original file causes a permission denied error in the Linux container.
On the Mac side the command had no effect with sed but would work with gsed that would need to be installed (e.g. with brew which is too much to ask...)

Docker +Mac option

As far as I can tell from the dates on github the last update of this tutorial was 7 years ago, and assumes that the user is in front of a complete GUI-based Linux computer.

To help the student follow all the steps, I have made an updated version of this tutorial that is mixing the Docker image rosettacommons/rosetta:latest with using a Macintosh binaries of Rosetta which would make computation faster for larger projects than running the Linux binaries within Docker. On a M-series Silicon Chip this would mean a double emulation:

1. change code from Linux to macOS
2. change code from Intel (amd64) to M-series (arm64) instructions

I have just finished this and it can be found at this page:
https://bcrf.biochem.wisc.edu/rosetta-ligand-docking/