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Cryo-EM Tutorial

This tutorial is the best newcomer path when the story is about density, model fit, and a map-oriented explanation rather than a pure structure-only scene.

What This Walkthrough Demonstrates

  • Opening a validated local cryo-EM map and its fitted model
  • Reviewing a global mesh-based fit before moving into sectional inspection
  • Using orthoplanes briefly as a real cryo check, not as the final presentation mode
  • Moving into a local heme-centered density cutaway and returning to a polished mesh hero

Recommended Target

ChimeraX is the recommended first cryo-EM target because the current map-fit workflow has the strongest mesh, orthoplane, and fit-quality presentation.

PyMOL remains a good alternative when you want a more tightly staged atomic handoff.

Prerequisites

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

Exact Command To Run

npm run showcase:chimerax:map

What You Should Expect To See

  • The local EMD-37575 map opens in ChimeraX as a clean mesh around the fitted hemoglobin model
  • The walkthrough holds a whole-assembly "model inside density" frame before fitting
  • The fit is executed and revisited from multiple angles so it feels like a real validation task
  • Orthoplane inspection appears briefly, then exits back to mesh
  • The scene tightens into a heme-centered local density cutaway and ends on a polished mesh-plus-model hero

First Commands To Say

  • "Open the cryo map and the fitted model."
  • "Keep the density as mesh and show the whole fitted assembly first."
  • "Run fitmap and rotate slowly around the fit."
  • "Clip into the heme neighborhood and keep the model visible inside the density."

Useful follow-ups:

  • "Show orthoplanes through the density briefly, then return to mesh."
  • "Compare the wide fit against the local cutaway."
  • "Save a polished map-fit export once the mesh hero looks balanced."

How To Run The Same Workflow Without Voice

npm run rehearse:workflow -- alphafold_to_cryo_handoff --target chimerax --capture --model examples/data/local/af-p69905.pdb --experimental examples/data/local/8wj1.cif --pae examples/data/local/af-p69905-pae.json --map examples/data/local/emd_37575.map

PyMOL Alternative

npm run showcase:pymol:cryo

Common Failure Points

  • The map takes a moment to load: wait for the workflow to complete before restyling manually
  • The orthoplane beat looks noisy: that is expected for the inspection phase; the workflow returns to mesh before the final hero frame
  • The local close-up feels too tight: recall the saved global fitted view first, then move back into the heme cutaway
  • You expected a synthetic map demo: this tutorial uses the real local cryo-EM map path
  • You want more prediction context first: start with AlphaFold Tutorial, then come back here
  • The target feels heavy for a first session: use the ligand pocket tutorial first, then return to cryo-EM

Where To Go Next

Generated Reference Pages