Rocco Moretti

You'll have to re-activate the virtual environment. That's just the `source .venv/bin/activate` stage of the installation instructions. I think that `uv` can also do the activation automatically if you use...

I'm not sure I understand your needs/use case. Best I can tell, what you want is handled by the contig map already. That is, if you have a pre-existing structure...

So you should be able to combine the motif scaffolding with the hotspot option already. But it sounds like what you're really after is a non-contact (avoidance?) potential -- instead...

Looks like things need to be beautified. (`python ../tools/python_cc_reader/beautify_changed_files_in_branch.py` from the source/ directory) Regarding the ga_ligand results change, does the beta_jan25 scorefunction pull in the ligand torsional changes from gen_potential,...

You should be able to use the "Resolve conflicts" button on the Github website to change things. (Just select the contents of main) Alternatively, just merge your branch with `main`...

Apologies. Here's [the direct link](https://downloads.rosettacommons.org/downloads/academic/2021/wk16/). ~We'll look into correcting the download link page soon.~ The main download page link should be fixed now.

Due to its size, Rosetta uses submodules for various things, most importantly dependencies. Gemmi is one of those. By default, Git does not pull down submodules when cloning a repository,...

Thanks for the clarification @cesarramirez -- PR #500 should fix this in the future. For existing clones, I think you can do a `git submodule set-url -- source/external/gemmi_repo https://github.com/project-gemmi/gemmi.git` (assuming...

@raroseroFAP Was there a question you had? It looks like you might have hit submit prematurely.

>Are the error messages popping up in integration tests rna_denovo_dna_bridge, swm_dna_bridge, posttranslationalmod_io expected from this change? The tests look like they still end the same though. That's not expected -...