Retain chain and residue numbering in RFdiffusion (#348) A number of issues (e.g., #103 , #171 , https://github.com/RosettaCommons/RFdiffusion/issues/312 , #315 ) have mentioned that RFdiffusion will change the chain IDs and residue numbering of the input structure. The designed chain ends up as chain "A", and the fixed chain(s) end up as chain "B". The numbering is also reset to start at 1. This can be particularly problematic in cases where comparisons to structures are needed, as well as multi-chain situations where all of the chains get fused. Inspired by @GCS-ZHN 's comment and solution referenced in Issue #103 , I've modified the code to maintain chain and residue numbering. In particular: Chains that are not "designable" will retain their original chain ID letters and residue numbers. Chains that are partially fixed (e.g., motif re-scaffolding) will retain their original chain ID letters. Residues will be re-numbered from 1 to length of chain. (It was not clear to me what the "correct" behaviour of chain residue numbering should be, given that the length of the chain and the position of any fixed residues might change.) Chains that are being fully generated de novo will be assigned the first available chain ID in the alphabet not used by any other chain. Residues will be numbered from 1 to length of chain.

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• rfd

Update README.md (#365) Update README to point to new [documentation resource](https://sites.google.com/omsf.io/rfdiffusion/overview). I also added some text in the Installation section to 1) specify that Sergey O.'s colab notebook only contains some of the features of RFdiffusion and 2) that there is now a Rosetta Commons-maintained docker image.

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• rfd

add GitHub CI workflow for running ppi-scaffolds tests (#1)

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• rfd

Update README.md

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• rfd

correct example

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• rfd

Update LICENSE

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Implemented inpaint_str and added example

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Added input pdb for p53 case

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Fixed incorrect variable name in contig parsing

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updating rosetta-ci test script, adding unpacking ppi scaffolds

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Update install instructions for model directory location. Be more specific about the location of the models directory. Addresses issue #80

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• rfd 「1」

Fixed model_only_neighbors typo

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• rfd 「1」

adding `pdb-diff` prefix to comparison test names

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• rfd 「1」

Finalize removing icecream as a dependency. Icecream was removed from the installation dependencies, but was still being imported (but not used).

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Added examples, and updated README

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