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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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The crystal lattice structure of a material allows us to determine how many molecules exist in its unit cell. With this information, alongside the unit-cell parameters - three distance parameters (a, b, c) and three angular parameters (α, β, γ).Density (ρ) = (Z × M) / (a × b × c × NA)where:Z is the number of formula units per unit cellM is the molar mass of the substancea, b, and c are the edge lengths of the unit cellNA is Avogadro’s numberFor a simple cubic lattice, atoms are located only at...
z Scores and Area Under the Curve01:17

z Scores and Area Under the Curve

z scores are the standardized values obtained after converting a normal distribution into a standard normal distribution. A z score is measured in units of the standard deviation. The z score tells you how many standard deviations the value x is above (to the right of) or below (to the left of) the mean, μ. Values of x that are larger than the mean have positive z scores, and values of x that are smaller than the mean have negative z scores. If x equals the mean, then x has a z score of zero.

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Related Experiment Video

Updated: Jun 4, 2026

Cryo-EM and Single-Particle Analysis with Scipion
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Cryo-EM and Single-Particle Analysis with Scipion

Published on: May 29, 2021

Scoring functions for cryoEM density fitting.

Daven Vasishtan1, Maya Topf

  • 1Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, University of London, London WC1E7HX, UK.

Journal of Structural Biology
|February 8, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces new scoring methods for fitting atomic models into cryo-electron microscopy (cryoEM) density maps. Mutual information and envelope scores show promise, potentially improving the accuracy and speed of cryoEM structure determination.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Cross-correlation function (CCF) is the standard for scoring atomic fits in cryo-electron microscopy (cryoEM) density maps.
  • Alternative scoring methods for cryoEM fitting are less explored but may offer advantages.

Purpose of the Study:

  • Introduce and evaluate novel scoring functions for cryoEM density fitting.
  • Compare the performance of new scores against established methods like CCF.
  • Assess the impact of Gaussian blurring width on fitting outcomes.

Main Methods:

  • Developed four new scoring functions for cryoEM fitting.
  • Benchmarked new and existing scores using simulated and experimental cryoEM maps of protein assemblies (including GroEL).
  • Assessed 1000 perturbed fits for each score against Cα RMSD to a reference structure.

Main Results:

  • Cross-correlation function (CCF) is a strong performer but can be improved or replaced in specific scenarios.
  • Mutual information score matches or exceeds CCF performance across most tests.
  • A novel 'envelope score' performs comparably to CCF at sub-nanometer resolution and is significantly faster.
  • Gaussian function width critically influences the fitting process.

Conclusions:

  • New scoring methods, particularly mutual information and envelope scores, offer viable alternatives or complements to CCF for cryoEM fitting.
  • The developed score-testing framework, combined with specific scores, can enhance cryoEM density fitting accuracy.
  • Understanding the impact of map generation parameters (e.g., Gaussian width) is crucial for optimal fitting.