Binder design with the target is pentamer symmetric center, not monomer

[Xiaowei160]

hi, i am using the rfdiffusion to design a peptide binder targeting the center pore of a pentamer protein (in the pentamer protein, each monomer contains four chains). this center pore is formed by 5 same chains (chain C) symmetricly as shown in the following image. the hot spots are two residues in each chain.

the script i use for the design:

source /home/user/miniconda3/etc/profile.d/conda.sh
conda activate SE3nv
python -u scripts/run_inference.py
inference.output_prefix="$RFD_OUTPUT_DIR/ppi"
inference.symmetry=c5
inference.input_pdb="/home/user/Desktop/test/3vbs.pdb"
'contigmap.contigs=[C1-11/0 12]'
'ppi.hotspot_res=[C6,C11]'
inference.num_designs=10
denoiser.noise_scale_ca=0
denoiser.noise_scale_frame=0

The output file always contains only one chain as target, not the pentamer pore.
How to modify the script to let it set the bind target as pentamer, not monomer?

[Xiaowei160]

i set the chain ID as from A to T, now the output file contains the pentamer pore. however, the 5 chains are linked as one chain! besides, some designed binder are not located in the center of the pore as the following image

the script i use now is:
python -u scripts/run_inference.py
inference.output_prefix="$RFD_OUTPUT_DIR/ppi"
inference.input_pdb="/home/user/Desktop/test/3vbs_modified.pdb"
'contigmap.contigs=[C1-11/0 G1-11/0 K1-11/0 O1-11/0 S1-11/0 5-12]'
'ppi.hotspot_res=[C6,C11,G6,G11,K6,K11,O6,O11,S6,S11]'
inference.num_designs=10
denoiser.noise_scale_ca=0
denoiser.noise_scale_frame=0

[rclune]

Is it adding peptide bonds to your input structure? (Not just a rendering issue or from the designed binder struture.)

RFdiffusion is not perfect, the designed binder will not always end up in the pore. Filtering steps are often recommended to pick the designs that meet your qualifications.

[Xiaowei160]

it linked the 5 chains together mathematically as one chain (not the rendering issue), which leads to the collapse in the following proteinmpnn and alphafold running.
this is a really tricky point for me in the rfdiffusion parameter setting.

how do you set the "contigmap" if you target pore is combined by several chains?