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Add current RamplotR preprint draft - #20
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Copilot review overview
🟡 Changes recommended
Two manuscript claims about insertion-code handling and ambiguous wwPDB alternates contradict the implementation.
Review effort: Balanced
Findings: 2
Open (2)
What changed in this PR
Adds a software-paper draft documenting RamplotR’s functionality, validation evidence, limitations, and reproducibility.
Changes:
- Adds the LaTeX manuscript and bibliography.
- Documents scope, build steps, and pre-submission tasks.
- Reports Bio3D, wwPDB, and pilot scaling results.
| File | Description |
|---|---|
paper/main.tex |
Adds the manuscript. |
paper/references.bib |
Adds cited references. |
paper/README.md |
Documents scope, build, and submission preparation. |
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| \subsection{Independent wwPDB evidence} | ||
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| For a deposited experimental structure, users can optionally attach the official wwPDB validation XML or compressed XML for the same entry and structural model \citep{Gore2017}. XML support is optional and requires the R package \texttt{xml2}. The parser reads residue records with explicit model, chain, residue number, insertion code, residue name and alternate-conformation information. Unlabelled alternates are preferred over alternate A, and ambiguous identities are not silently assigned. |
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| \subsection{Numerical cross-check against Bio3D} | ||
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| Two real structures were used to cross-check the custom backbone implementation against Bio3D torsion calculations \citep{Grant2006}: the 46-residue crambin structure 1CRN and the SARS-CoV-2 spike structure 6VXX. Residue identifiers were normalized only for surrounding whitespace; insertion-code distinctions were retained and duplicate keys were rejected. Coverage was calculated over \ramplotr-eligible residues and finite angles, rather than every row returned by Bio3D. |
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Adds the RamplotR manuscript as a clean paper-only branch rebased onto current
main.The draft is synchronized to software revision
6d1e4e95cdf5df4ae63bdbeccb4a6eeb7af41a1aand describes the current tool rather than older/legacy calculations.Current scientific/software scope in the manuscript:
The paper explicitly positions RamplotR as a focused backbone-conformation workbench rather than a replacement for MolProbity/Phenix/Coot/PDBe or other comprehensive validation/model-building environments.
Only three files differ from current
main:paper/main.tex,paper/references.bib, andpaper/README.md.Before submission: review authors/contributions, add funding/acknowledgements, choose a publication release/tag and immutable archive/DOI, and consider whether to expand the five-structure functional validation set or add a dedicated comparison/ensemble workflow figure.