The cyclic peptides generated by RFdiffusion are not closed.

[zunyi-zhang]

I can't obtain the correct cyclic peptide backbone pdbs, when I use the RFdiffusion pipeline.
All the cyclic peptides generated by RFdiffusion are not closed at their C-terminus and N-terminus, which just have a cyclic conformation. I use the standard pipeline provided by RFdiffusion authority. Show you below:

python /HOME/scz0bp0/run/zzy/RFdiffusion/scripts/run_inference.py
--config-name base
inference.output_prefix=/HOME/scz0bp0/run/zzy/output/RFdiffusion_output/xxx
inference.num_designs=10
'contigmap.contigs=[10 A18-132/0]'
inference.input_pdb=/HOME/scz0bp0/run/zzy/input/xxx.pdb
inference.cyclic=True
diffuser.T=50
inference.cyc_chains='a'
ppi.hotspot_res=['A56','A58','A113','A115','A121','A123'] \

[TimothyChen225]

If you are using PyMOL, please use the command 'show sticks, chain A'. (Assuming the peptide belongs to chain A).