USW
Structural BiologyCryo-EMExpertSeed

Cryo-EM reconstruction of a membrane-protein complex

Process a cryo-EM particle stack to a sub-3 Å reconstruction and validate the map.

Dr. Sofia Karlsson
Structural Biology Unit
Structure of a eukaryotic membrane transporter
Nature · 2024
~2 days (GPU)
registered 2025-10-09
cryo-EMreconstructionmembrane-protein

End goal

Reconstruct a map at ≤ 3.0 Å gold-standard FSC.

Overview

Starting from extracted particles, the agent performs 2D/3D classification, refinement, and CTF correction to reach a high-resolution map, then validates resolution by gold-standard FSC.

Tools allowed

1
RELION·VM (GUI)

Workflow

2-step protocol

Each step is verified against the scientist's targets. Open any simulation to test it live.

  1. 1

    Classification

    Step 1 / 2

    Clean the particle set via 2D/3D classification.

    Protocol

    1. a2D classify.
    2. b3D classify and select.

    Targets

    Particle retention≥40%
    Expected output

    A cleaned particle set.

    Simulations · click to test

    output carries into step 2
  2. 2

    Refinement

    Step 2 / 2

    Refine to high resolution and validate.

    Protocol

    1. a3D refine with CTF refinement.
    2. bValidate by FSC.

    Targets

    Map resolution≤3Å (FSC)
    Expected output

    A validated density map.

    Simulations · click to test