RosettaCommons / RosettaCommons/RFdiffusion
why cyclic peptide doesnt work for chain b
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Description
Hi , I am trying to follow the given example for macrocyclic binder but I was trying to make the binder cyclize in chain b, so what i provide is
python $script
inference.output_prefix=$prefix
inference.num_designs=$num_designs
'contigmap.contigs=[12-14 A3-117/0 ]'
inference.input_pdb=$pdb
++inference.cyclic=True
diffuser.T=50
++inference.cyc_chains='b'
ppi.hotspot_res=['A51','A52','A50','A48','A62','A65']
I just change the order if contigs and the chain to be cyclic. the rest are exactly the same as the given example. however i cant get a cyclic binder with this. I am obviously specifying something wrong but havent figured out what yet. Could you please help me
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Research direction
Reproduce the reported command using the RFdiffusion inference entry point referenced as $script, keeping the contig order and ++inference.cyc_chains='b' setting. Trace how cyclic-chain and contig options are handled; done means the command produces a cyclic binder for chain B or clearly identifies the invalid setting.
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Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100