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Related Experiment Video

Updated: Jul 24, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.4K

Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation.

Vladimir Y Lunin1, Natalia L Lunina1, Alexandre G Urzhumtsev2,3

  • 1Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 1, Professor Vitkevich St., Pushchino, 142290, Russia.

Current Research in Structural Biology
|July 10, 2023
PubMed
Summary

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Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM.

bioRxiv : the preprint server for biology·2026
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Explicit correction of severely non-uniform distributions of cryo-EM views.

Acta crystallographica. Section D, Structural biology·2026
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Direct calculation of variable-resolution maps by fully analytic approximations to atomic images.

Journal of applied crystallography·2026
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Quantifying distributions of cryo-EM projections.

Acta crystallographica. Section D, Structural biology·2026
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Rescaling FSC curves.

Acta crystallographica. Section D, Structural biology·2025
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The separation of the effects of atomic displacement and local resolution in crystallographic and cryo-electron microscopy maps.

Acta crystallographica. Section A, Foundations and advances·2025
This summary is machine-generated.

This study introduces a new method to analyze atomic heterogeneity in X-ray crystallography and cryo-electron microscopy (cryo-EM) maps. It accurately estimates local resolution and atomic displacement parameters, improving structural biology insights.

Area of Science:

  • Structural Biology
  • Biophysical Chemistry
  • Computational Biology

Background:

  • Experimental structural biology maps (X-ray crystallography, cryo-EM) often exhibit regional heterogeneity in detail.
  • This heterogeneity complicates accurate atomic interpretation and model refinement.

Purpose of the Study:

  • To develop and validate a method for quantifying local heterogeneity in structural biology maps.
  • To simultaneously estimate atomic displacement parameters and local map resolution.

Main Methods:

  • A local real-space procedure was developed to estimate heterogeneity parameters for individual atoms.
  • The method utilizes an analytic representation of the atomic image based on inhomogeneity parameters and atomic coordinates.
  • Tested on both simulated and experimental crystallographic and cryo-EM density maps.
Keywords:
Atomic imagesInhomogeneous resolutionReal-space refinementShell decomposition

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Main Results:

  • The method accurately determines local map resolution and atomic displacement parameters for simulated heterogeneous maps.
  • For experimental maps, estimated local resolutions align with global resolutions.
  • Estimated atomic displacement parameters closely match refined model values for experimental data.

Conclusions:

  • The proposed method effectively characterizes and quantifies local resolution and atomic displacement in heterogeneous structural maps.
  • Successful application to experimental data demonstrates its practical utility in X-ray crystallography and cryo-EM.
  • This approach enhances the interpretation and refinement of complex structural models.