Diffusion of unindexed fixed residues islands with unindexed unfixed island

I've been using RFD3 to build scaffolds around 3 motifs or residue islands that I want fixed in place as in my input .pdb., which works great. However, I also want to include a small sequence tag that is unindexed (placed anywhere in the structure) and is not fixed in place, i.e. can contribute to the scaffold of the residue islands and structure is not conserved, but have the sequence conversed.

The documentation states "Unindexed atoms are always fixed unless otherwise specified in the select_fixed_atoms option. At least one atom in any unindexed residue needs to be fixed". Would it be possible to allow unindexed residues to not be fixed at all? Allowing the model to place my sequence within the scaffold where it saw fit.

Start by reading the RFD3 documentation on unindexed atoms and the select_fixed_atoms option, then trace how unindexed residues are handled. Done means an unindexed sequence tag can be placed freely without preserving its input structure, while the indexed fixed residue islands remain fixed and the tag sequence is retained.