Motif Scaffolding Question

Hi,

In our initial testing of scaffold generation with two idx ranges, we see that after running the results through Alphafold our top results superimpose well to the reference structure, but the motifs are in the wrong locations (despite superimposing quite well). Additionally, it looks like the distance between these two ranges are always fixed. Is there anyway to run with a flexible distance between two motif scaffolds or any suggestions on ways to ensure the motifs remain positioned properly when aligned to reference structures?

Start with the scaffold-generation entry point and the handling of two idx ranges described here; reproduce the result through AlphaFold and compare motif placement and inter-range distance with the reference structure. Done means the supported behavior for flexible distances and preserving motif positions is clearly defined and demonstrated, or the issue is narrowed to a concrete change.

Written by the indexing model from the issue text.