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AlphaFold Tutorial

This tutorial is the best newcomer entry point if you want to see BioVoice handle prediction-versus-experiment work rather than a generic scene demo.

What This Walkthrough Demonstrates

  • Opening a validated local AlphaFold model and experimental comparison target
  • Moving from global assembly context into a local overlay story
  • Running the same workflow with voice or without voice

Recommended Target

ChimeraX is the recommended first AlphaFold target because the current overlay path has strong named views, readable assembly context, and a polished comparison handoff.

PyMOL remains a strong alternative and is linked below.

Prerequisites

  • npm install
  • npm run prepare:data
  • npm run generate:examples
  • Local .env with OPENAI_API_KEY for live voice

Exact Command To Run

npm run showcase:chimerax:overlay

This launches the validated local AlphaFold-versus-experiment overlay showcase using demo data already bundled in examples/data/local/.

What You Should Expect To See

  • The experimental 4HHB tetramer opens in ChimeraX
  • The AlphaFold hemoglobin alpha-chain model opens and aligns into the same scene
  • The walkthrough moves from full-assembly context into a local comparison patch
  • A polished export is available at the end of the recipe

First Commands To Say

  • "Open the experimental tetramer and the AlphaFold chain model."
  • "Color by confidence."
  • "Compare the prediction to the experimental backbone near the heme."

Good follow-ups:

  • "Keep the whole complex visible but emphasize the comparison chain."
  • "Pull the prediction slightly to the right for a cleaner side-by-side."
  • "Save a polished export."

How To Run The Same Workflow Without Voice

npm run rehearse:workflow -- alphafold_vs_experiment_overlay --target chimerax --capture --model examples/data/local/af-p69905.pdb --experimental examples/data/local/4hhb.pdb

PyMOL Alternative

npm run showcase:pymol:overlay

Common Failure Points

  • You forgot the demo data step: rerun npm run prepare:data
  • You expected another voice provider: AlphaFold live voice still runs through OpenAI Realtime only
  • The overlay looks too busy: use the saved workflow views and keep the non-focused chains subdued
  • You want confidence-first rather than overlay-first: use the scientific workflow catalog and start with the confidence review instead

Where To Go Next

Generated Reference Pages