Running RFD3 - partial diffusion format issue

[Yuzhe-Chen7221]

Question 1.RFD1 provided script named design_partialdiffusion_withseq.sh, which showed how to optimize binder against a peptide target. However, there is no similar script in RFD3.

Describe the issue/question
The AF3 prediction output were used as input to partial diffusion by RFdiffusion3. In PDB, the binder is A1-A70 and target is B1-B400. Could you provide standard and detailed json file? For example
{
"GUCY2C_binder3_partial_diffusion": {
"dialect": 2,
"input": "./xxx.pdb",
"partial_t": 10.0,
"contig": "A1-70,/0,B1-B400",
"select_fixed_atoms": "B1-B400",
"select_unfixed_sequence": "A1-70,/0"
}
}

Question 2. Could RFD3 be used for scaffold-guided binder design?