RosettaCommons / RosettaCommons/RFdiffusion
Contigs in google colab vs Contigs in github during binder design
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- Python
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Description
I've been having some difficulties with the format in which the pdb files are output from rfdiffusion, where the designed binder is output as chain A rather than chain B which seems to cause some issues for proteinMPNN later on. I noticed that the google colab version seems to fix this by omitting the /0 when specifying the config options, and then running fix_pdb() on the outputs to fix the chains, is this correct?
If so, I wanted to confirm whether this is also a better way to run the code locally or if some further setup is required such that config doesn't need /0 specified to design binders properly?
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Research direction
Compare the Google Colab and local binder-design configuration, focusing on omitting /0 and applying fix_pdb() to the outputs. Reproduce the chain-A versus chain-B result, then verify whether the resulting PDB is accepted by ProteinMPNN and document whether local setup needs additional configuration.
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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