version: "1.0.0" name: rfd4-proteina-annotated-cif description: > Create, inspect, explain, modify, and validate annotated CIF/mmCIF inputs for RFProteina with AtomWorks Python APIs. Use automatically for any question or task involving an existing annotated CIF, adding or changing conditioning, selecting fixed backbone or motif atoms, indexing/unindexing residues, hotspots, RASA, H-bonds, internal-coordinate groups, centroids, expandable segments, bonds, charges, combining annotated structures, or preparing a structure file as an annotated CIF. license: See the RFProteina repository (Baker Lab x NVIDIA collaboration)

RFProteina annotated CIF authoring

An annotated CIF is a structure plus AtomWorks StandardAnnotation columns that encode the RFProteina design problem. Prefer direct Python manipulation of an AtomArrayPlus: parse, derive selection annotations, set conditions, validate, write, and round-trip. Visually inspect chemistry and intent, especially for ligands, metals, PTMs, or PDB sources.

This skill defines CIF authoring semantics. Workspace instructions and the active campaign govern shared-input ownership, output locations, length materialization, generation, and database accounting. Authoring a CIF does not by itself authorize a generation run or establish a campaign ledger policy.

Workflow

1. Inspect the source, existing conditions, requested assembly, and design intent.

Ask only about ambiguities that change the design problem. For PPI, recommend backbone-only internal coordinates plus full target sequence and requested hotspots; preserve explicit alternatives and existing benchmark inputs.

1. Read python-authoring.md for registry import,

parser selection, condition edits, expandable segments, and combining arrays.

1. Read annotators-and-selections.md

when translating structural intent into atom masks or checking installed annotation support.

1. Use the canonical condition reference

and interaction rules for condition levels, values, and model support. Do not infer support from an annotation's ability to round-trip.

1. Complete validation.md, including chemistry and

indexing review, pre-save checks, and save/reload comparison.

For a saved CIF, use bash skills/rfd4-proteina-annotated-cif/scripts/inspect_cif.sh <file.cif> to inventory its structure, chemistry, expandable segments, and conditions. Use bash skills/rfd4-proteina-annotated-cif/scripts/check_annotated_cif.sh <file.cif> for pipeline validation and chemistry checks. Both helpers are read-only; see the validation reference for options and limits.

Output standard

Return the annotated CIF artifacts required by the task, identifying source templates and any sampled children. Report input provenance and parse preset, selections and conditioning counts, segment and chemistry edits, validation results, and any unresolved scientific ambiguity.