Multiple active site scaffolding is possible?

[sj584]

In a recent paper from RFdiffusion author, Joseph L. Watson, Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning (https://www.biorxiv.org/content/10.1101/2024.05.07.592871v1.full.pdf)

It seems like RFjoint2 can inpaint single scaffold for three different activate sites generated from three different PDB (RSV epitopes).

So I tried to perform the same procedures but RFDesign github says it is better to do RFdiffusion since it performs better.

The same process is possible also in RFdiffsuion? The current motif-scaffolding script example in the github seems to have only one PDB as input.

Thanks