docs: document chain-internal ncAAs via userCCDPath and protein modifications#662
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Fred-Jing wants to merge 1 commit intogoogle-deepmind:mainfrom
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docs: document chain-internal ncAAs via userCCDPath and protein modifications#662Fred-Jing wants to merge 1 commit intogoogle-deepmind:mainfrom
Fred-Jing wants to merge 1 commit intogoogle-deepmind:mainfrom
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docs: add example for chain-internal ncAAs via userCCDPath
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Summary
This PR adds a short documentation example for using a user-provided CCD component as a chain-internal non-canonical
amino acid via
protein.modifications.The code path already supports this workflow, but
docs/input.mdcurrently documents protein modifications and user-provided CCDs mainly as separate concepts, and the user-provided CCD section is currently framed around custom
ligands.
This patch adds:
User-provided CCDuserCCDPath + protein.modificationsbondedAtomPairsWhy
Without an explicit example, it is easy to assume that
userCCDPathis only intended for ligands, or that chain-internal ncAAs should be modeled as ligands rather than polymer modifications.
Testing
Documentation-only change.
I also manually validated this workflow on a local AlphaFold 3 installation by running inference with custom peptide-
linking components referenced through
protein.modificationsand supplied throughuserCCDPath.AI usage disclosure
This PR text and the initial draft wording were prepared with AI assistance, then manually reviewed and edited before
submission.