Rachel Clune

I unfortunately cannot find a link to Stephen Rittie's CoLab notebook. Have you tried running RFdiffusion outside of a notebook? If you are not running on ARM-based systems the [Docker...

There is an example for designing symmetric oligomers in the README (specific section [here](https://github.com/RosettaCommons/RFdiffusion/tree/main?tab=readme-ov-file#generation-of-symmetric-oligomers)) and example scripts, namely `design_cyclic_oligos.sh` and `design_tetrahedral_oligos.sh` in the [examples folder](https://github.com/RosettaCommons/RFdiffusion/tree/main/examples). Are these examples useful?

> yes the code is working when attempting to run from a Google Colab notebook that Stephen Rettie set up. indeed the cyclic nature of the peptides is more obvious...

Can you provide more details about the settings you were using in you calculation? Do you have [hbplus](https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/) installed and your environment paths set correctly? There are instructions for this...

Can you provide more details so that we can try to recreate this error?

The option name is `select_unfixed_sequence` not `select_unfixed_seq`.

COM stands for center of mass. The ORI token specifies where the center of mass of your designed structure should be.

Were you expecting an output like RFdiffusion (the original) where all of the residues in the designed portions were glycines? RFD3 operates on the atom level instead of the residue...

Can you clarify what you mean by the 'python command'?

Can you say more about what is not working? Are you getting an error message or unexpected outputs? If you are just trying to add 20 residues to the start...