Rocco Moretti

In contig specifications, when you specify a range for generated structures, this is a range of potential lengths, which is randomly sampled. For example, if you have 'contigmap.contigs=[A10-25/27-32]', RFdiffusion will...

It might be better to use the user directory as a fall back. That is, instead of *always* writing to the user directory, only use the user directory if the...

To further clarify, a non-commercial license comes automatically with the download. You should be able to just omit the `USERNAME:PASSWORD@` in the conda URL.

> IIRC, there are similar functions in the pyrosetta.distributed module. May be nice to make sure they do the same thing/call the same code under the hood. From what I...

> One thing I’ve repeatedly found myself doing over the years is parsing Rosetta score files into a more structured format—usually JSON. Jared added the ability to make JSON-formatted scorefiles...

The dgl module should be installed when you [install](https://github.com/RosettaCommons/RFdiffusion?tab=readme-ov-file#getting-started--installation) RFdiffusion -- in particular, it's installed when you run the `pip install --no-cache-dir -r requirements.txt` line. Note that the installation happens...

Note that this likely shouldn't be merged until we figure out how to fix it.

To save on computation, the ScoreFunction does a bunch of caching of energies, and only recomputes things as needed. This caching happens in the Energies object. I'm guessing that's what's...

I'll leave it to others to provide more details about the exact parameters used with the paper, but you'll likely get decent results using MMseqs2-generated MSAs. (This is what most...

You should be able to use CCD codes in the `seq:` lines if you enclose them in parenthesis -- See, for example, the [3en2_from_json_with_msa.json](https://github.com/RosettaCommons/modelforge/blob/production/docs/rf3/examples/3en2_from_json_with_msa.json) example. I believe that should work...