RosettaCommons / RosettaCommons/RFdiffusion
Question Regarding the Use of Hotspot Option in Motif Scaffolding
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Description
Hello, thank you for creating such a great model.
I am currently redesigning part of an existing Binder.
My task involves designing a portion of Chain B, while Chain A remains fixed. I've utilized motif scaffolding and incorporated some residues of Chain A as hotspots.
I entered it as follows :
'contigmap.contigs=[A1-224/0 B1-97/'"${k}"'-'"${k}"'/B105-116]' 'ppi.hotspot_res=[A139,A141,A142,A199,A201]'
My question is this:
How can I confirm whether RFdiffusion is actually incorporating these hotspots in the design?
I indirectly verified that the Hotspot option wasn't ignored because the log shows that 'Complex_base_ckpt.pt' is being used.
However, since all example Binder designs are about designing an entirely new Chain, I'm not sure if my input script is working as intended. I'm quite new to this field and not yet proficient in reading code.
Can RFdiffusion operate in the way I intend? Or is there another method to check whether hotspots are being used?
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Research direction
Review the motif-scaffolding and binder-design examples alongside the contigmap.contigs and ppi.hotspot_res arguments. Compare the fixed Chain A and designed Chain B setup with those examples, then inspect the run log's Complex_base_ckpt.pt entry. Done means documenting whether this input mode supports hotspots and a reproducible check that confirms their use.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100