Hi,

I was wondering if structure refinement could be performed with Chroma (technically similar to partial diffusion in RFDiffusion, but full-atom). With this notebook, I tried to do at the Conditional generation part, using this code:
chroma = Chroma()
protein = Protein("1xyz", device="cuda")
substructure_conditioner = conditioners.SubstructureConditioner(
protein=protein,
backbone_model=chroma.backbone_network,
selection='chain A or chain B'
).to("cuda")

new_protein = chroma.sample(
protein_init=protein,
conditioner=substructure_conditioner,
langevin_factor=4.0,
langevin_isothermal=True,
inverse_temperature=8.0,
sde_func="langevin",
steps=50
)

This gave me almost identical structures, with some side-chains changed. However, I understand that the SubstructureConditioner will keep everything totally fixed which is not my aim, but I did not find a conditioner to allow for some movement, not totally fixing the input. I tried to look in the underlying code but could not yet find where to start modifying it for more flexibility (also for flexible design). Is this even possible?

I would be grateful for any help that you can provide on this matter.