RosettaCommons / RosettaCommons/RFdiffusion

chain break doesn't work as expected

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Description

I thought that if I add /0 in contig, that segment will become a separated chain in the result protein. for example ,
'contigmap.contigs=[A229-445/0 B230-444/0 20-20/C70-328/50-50]' , RFDiffusion will generate 3 chains. However I only get two chains in the result, Chain A and Chain B are merged.

I tried to separate Chain A and Chain B by a new contig(chain order is A C B): [A229-445/0 20-20/C70-328/50-50/0 B230-444/0 ], I still got the same result, i.e. target chains were merged to one chain.

I also tried a RFDiffusion wrapper from Sergey's colabdesign, I found he removed all the chainbreaks(/0), RFDiffusion only generates a single chain for both target and binder, then he uses 'run_mpnn_only.py' to separate this single chain to 3 chains.

I'd like to know if it is possible that RFDiffusion generates 3 chains based on provided chain break in contig.

Thanks
Bin

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Research direction

Reproduce the reported contigmap.contigs examples and compare the generated chains with the expected three-chain result. Read the RFdiffusion chain-break handling around contig parsing and compare it with the mentioned run_mpnn_only.py workflow. Done means determining whether /0 should preserve separate output chains and documenting or correcting the observed behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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