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Scientific Workflows

This catalog is the task-first launch layer for AlphaFold and Rosetta work.

If you want a guided newcomer walkthrough first, start with:

Use it from the UI Scientific Launch rail, or pass the workflow explicitly to the agent start path.

Common Launch Pattern

  • npm run agent:start -- <pymol|chimerax> --workflow <workflowId> [scientific inputs]
  • Examples: --uniprot, --model, --experimental, --pae, --map, --bundle, --scorefile, --top-n
  • Keep Push To Talk as the default until the first clean live turn is complete.

Validated Local Showcases

These are the strongest local-data rehearsals to run before a live demo or voice session:

  • npm run showcase:pymol:pocket
  • npm run showcase:pymol:overlay
  • npm run showcase:pymol:cryo
  • npm run showcase:pymol:rosetta
  • npm run showcase:chimerax:pocket
  • npm run showcase:chimerax:overlay
  • npm run showcase:chimerax:map
  • npm run showcase:chimerax:rosetta

Run npm run verify:showcases to rehearse the pocket, AlphaFold, cryo, and Rosetta showcase matrix on both targets.

AlphaFold Confidence Review

Start from a confidence-colored prediction, isolate uncertain loops, and keep the scene ready for a fast PTT demo.

  • Default target: chimerax
  • Intent: confidence review
  • Voice starter: Open the local AlphaFold model and color it by confidence.

Input Hints

  • uniprot
  • model
  • pae

Ranked Candidate Recipes

  • chimerax: chimerax-alphafold-confidence-review (100) - Best named-view confidence review and loop isolation.
  • pymol: pymol-alphafold-confidence-sweep (98) - Best putty-style confidence sweep and export.

Launch Example

  • npm run agent:start -- chimerax --workflow alphafold_confidence_review --uniprot P12345 --model ./model.pdb

Operator Notes

  • Use this when you want the first story beat to be confidence and flexibility.
  • Best for a clean overview, a loop close-up, and a high-confidence export.

AlphaFold vs Experiment Overlay

Overlay a prediction against an experimental structure, preserve assembly context, and move into a focused comparison patch.

  • Default target: chimerax
  • Intent: prediction versus experiment
  • Voice starter: Open the experimental tetramer and the AlphaFold chain model.

Input Hints

  • uniprot
  • model
  • experimental

Ranked Candidate Recipes

  • chimerax: chimerax-alphafold-experimental-overlay (100) - Best overlay handoff with named views.
  • pymol: pymol-alphafold-experimental-overlay (99) - Best chain-level overlay and polished export.

Launch Example

  • npm run agent:start -- chimerax --workflow alphafold_vs_experiment_overlay --uniprot P12345 --model ./model.pdb

Operator Notes

  • Use this when the demo needs a direct structural comparison, not just a confidence story.
  • The best shots are an assembly overview, an aligned overlay, and a side-by-side comparison.

AlphaFold Multimer Interface Review

Inspect a multimer interface, surface the contact shell, and keep the comparison anchored while the interface is explained.

  • Default target: chimerax
  • Intent: interface triage
  • Voice starter: Open the AlphaFold multimer and isolate the interface shell.

Input Hints

  • uniprot
  • model
  • pae

Ranked Candidate Recipes

  • chimerax: chimerax-interface-contacts-analysis (100) - Best interface contact, clash, and hbond review.
  • chimerax: chimerax-alphafold-confidence-review (82) - Good fallback for confidence-colored triage.
  • pymol: pymol-crystal-packing-contacts (72) - Useful if the comparison needs a PyMOL-style pocket or packing shell.

Launch Example

  • npm run agent:start -- chimerax --workflow alphafold_multimer_interface_review --uniprot P12345 --model ./model.pdb

Operator Notes

  • Use this when the story is about contacts, clashes, or an interface shell inside a prediction.
  • The model should stay readable while only the interface becomes the focus.

AlphaFold PAE-Guided Triage

Use optional PAE input to prioritize uncertain regions and turn them into a short, presentation-ready triage story.

  • Default target: chimerax
  • Intent: PAE triage
  • Voice starter: Show me the uncertain AlphaFold regions first.

Input Hints

  • uniprot
  • model
  • pae

Ranked Candidate Recipes

  • chimerax: chimerax-alphafold-confidence-review (100) - Best confidence triage and named-view summary.
  • pymol: pymol-alphafold-confidence-sweep (96) - Best putty-based uncertain-region sweep.

Launch Example

  • npm run agent:start -- chimerax --workflow alphafold_pae_guided_triage --uniprot P12345 --model ./model.pdb

Operator Notes

  • Use this when you want the workflow to surface uncertainty before moving into the overlay.
  • The UI should summarize low-confidence regions and keep the rest of the assembly quiet.

AlphaFold to Cryo Handoff

Move from prediction or confidence review into a cryo-plus-atomic presentation without losing the scene context.

  • Default target: pymol
  • Intent: cryo handoff
  • Voice starter: Show the cryo map and keep the atomic model visible for the handoff.

Input Hints

  • experimental
  • map
  • pae

Ranked Candidate Recipes

  • pymol: pymol-cryo-atomic-handoff (100) - Best cryo-plus-atomic hero story in PyMOL.
  • chimerax: chimerax-em-map-fit-demo (96) - Best map-fit and cutaway handoff in ChimeraX.

Launch Example

  • npm run agent:start -- pymol --workflow alphafold_to_cryo_handoff --uniprot P12345 --model ./model.pdb

Operator Notes

  • Use this when the model needs to read against a density map or an assembly cutaway.
  • Best for a dense but visually polished before/after handoff.

Rosetta Scaffold / Design Review

Compare a scaffold against a design candidate, keep the scaffold anchored, and explode the design cleanly for the before/after shot.

  • Default target: pymol
  • Intent: design review
  • Voice starter: Open the scaffold and design candidate and keep the scaffold quiet.

Input Hints

  • model
  • bundle

Ranked Candidate Recipes

  • pymol: pymol-rosetta-style-design-review (100) - Best exploded scaffold-versus-design comparison in PyMOL.
  • chimerax: chimerax-rosetta-style-design-review (98) - Best semantic-handle design review in ChimeraX.

Launch Example

  • npm run agent:start -- pymol --workflow rosetta_scaffold_design_review --bundle ./bundle --scorefile ./score.sc --top-n 5

Operator Notes

  • Use this for scaffold-versus-design storytelling with strong semantic handles.
  • Best when the key question is what changed in the remodeled shell.

Rosetta Interface Packing Review

Focus on interface contacts, packing, clashes, and residue neighborhoods before the final export.

  • Default target: chimerax
  • Intent: interface packing
  • Voice starter: Show the interface contacts and clashes around the design patch.

Input Hints

  • bundle
  • scorefile
  • topN

Ranked Candidate Recipes

  • chimerax: chimerax-interface-contacts-analysis (100) - Best contacts, clashes, and hbond interface analysis.
  • pymol: pymol-crystal-packing-contacts (92) - Best packing-shell and contact storytelling in PyMOL.
  • chimerax: chimerax-rosetta-style-design-review (86) - Best if you want the interface review folded into the scaffold/design story.

Launch Example

  • npm run agent:start -- chimerax --workflow rosetta_interface_packing_review --bundle ./bundle --scorefile ./score.sc --top-n 5

Operator Notes

  • Use this when the science story is about interaction quality, not just a static overlay.
  • Best for packed interfaces, contacts, and clash cleanup.

Rosetta Ligand Redesign Review

Tell a ligand-pocket redesign story with the pocket bright, the scaffold subdued, and the remodeled shell clearly visible.

  • Default target: pymol
  • Intent: ligand redesign
  • Voice starter: Keep the ligand bright and show only the redesigned shell.

Input Hints

  • model
  • bundle
  • scorefile

Ranked Candidate Recipes

  • pymol: pymol-binding-pocket-story (100) - Best pocket storytelling and ligand emphasis.
  • pymol: pymol-rosetta-style-design-review (90) - Best if the redesign is part of a broader scaffold overlay.
  • chimerax: chimerax-interface-contacts-analysis (75) - Good contact cleanup when the ligand pocket is part of a larger interface.

Launch Example

  • npm run agent:start -- pymol --workflow rosetta_ligand_redesign_review --bundle ./bundle --scorefile ./score.sc --top-n 5

Operator Notes

  • Use this when the design is centered on a binding site or catalytic pocket.
  • Best for a pocket hero shot, interaction shell, and polished export.

Rosetta Top-Design Compare

Rank the top designs, load the winners, and move between the overview and the best-scoring comparison shot.

  • Default target: pymol
  • Intent: top design compare
  • Voice starter: Rank the top designs and open the best-scoring candidates.

Input Hints

  • bundle
  • scorefile
  • topN

Ranked Candidate Recipes

  • pymol: pymol-rosetta-style-design-review (100) - Best design-versus-scaffold compare in PyMOL.
  • chimerax: chimerax-rosetta-style-design-review (98) - Best if you want named views and interface handoff in ChimeraX.
  • pymol: pymol-two-structure-comparison (84) - Useful fallback for a plain structural compare when design metadata is limited.

Launch Example

  • npm run agent:start -- pymol --workflow rosetta_top_design_compare --bundle ./bundle --scorefile ./score.sc --top-n 5

Operator Notes

  • Use this when the input bundle already contains multiple candidates and the best one is not obvious.
  • Best for scorefile-driven review and side-by-side design comparison.