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.
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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