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Projects and scientific interpretation
Save a portable .proteonator file with immutable sources, hashes, sequence/chemistry states, coding candidates, correspondence, evidence, scenarios, maps, frames, measurements, views and methods. Compression has bounded expanded size. Earlier formats open into new copies; historical results keep their original methods.
Autosave waits for operations to finish and retains two bounded generations. Recover opens a copy; an unreadable latest snapshot falls back to the earlier valid copy with an explicit message. Save As preserves it. Saved projects are not automatically overwritten by recovery. Recent previews/preferences are local convenience data and cannot replace project integrity checks.
A constructed state is a hypothesis. A desired product formula is not evidence of manufacturing success. A contact is proximity, a local minimum is not an equilibrium ensemble, and a camera movie is not molecular dynamics. Raw energy differences between differently composed systems are not affinity.
Back-translation cannot recover a native transcript or historical tRNA. RNA folding does not determine RNA family or expression yield. An imported annotation retains its original evidence scope; it does not become experimental proof through display.
For complete units, guards, algorithm/settings, chemistry scope and references, read Scientific methods. Original code is MIT; bundled components retain their own terms, including ViennaRNA/NAVIEW restrictions. No institutional endorsement is implied.