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Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
X-ray Crystallography02:18

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Electron Orbital Model01:18

Electron Orbital Model

Orbitals are the areas outside of the atomic nucleus where electrons are most likely to reside. They are characterized by different energy levels, shapes, and three-dimensional orientations. The location of electrons is described most generally by a shell or principal energy level, then by a subshell within each shell, and finally, by individual orbitals found within the subshells.The first shell is closest to the nucleus, and it has only one subshell with a single spherical orbital called the...
Overview of Electron Microscopy01:25

Overview of Electron Microscopy

The wavelengths of visible light ultimately limit the maximum theoretical resolution of images created by light microscopes. Most light microscopes can only magnify 1000X, and a few can magnify up to 1500X. Electrons, like electromagnetic radiation, can behave like waves, but with wavelengths of 0.005 nm, they produce significantly greater resolution up to 0.05 nm as compared to 500 nm for visible light. An electron microscope (EM) can create a sharp image that is magnified up to 2,000,000X.

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Related Experiment Video

Updated: Jun 22, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions.

Xavier Siebert1, Jorge Navaza

  • 1Mathematics and Operational Research, Polytechnic Institute of Mons, 9 Rue de Houdain, 7000 Mons, Belgium. xavier.siebert@fpms.ac.be

Acta Crystallographica. Section D, Biological Crystallography
|July 1, 2009
PubMed
Summary

New graphical software enables interactive fitting of atomic models into electron microscopy maps. This tool enhances near-atomic resolution interpretation of macromolecular structures and their component interactions.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Related Experiment Videos

Last Updated: Jun 22, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Electron microscopy (EM) provides 3D reconstructions of macromolecular structures.
  • Near-atomic resolution interpretation requires fitting atomic models into EM maps.
  • Existing methods may lack efficiency or interactivity for complex structures.

Purpose of the Study:

  • To present novel graphical software for interactive atomic model fitting into EM reconstructions.
  • To improve the interpretation of macromolecular structures at near-atomic resolution.
  • To facilitate the study of component interactions within complexes.

Main Methods:

  • Reciprocal space calculations for fast algorithms.
  • Real-time correlation computation and display during graphical model placement.
  • Least-squares minimization for refinement of model positions and orientations.
  • Normal-mode calculations for simulating conformational changes.

Main Results:

  • Software demonstrated effective application across various symmetries and resolutions.
  • Fast algorithms enabled the use of entire reconstructions.
  • Interactive fitting and real-time feedback facilitated model placement and refinement.
  • Simulation of conformational changes provided insights into dynamic aspects.

Conclusions:

  • The developed software offers an efficient and interactive solution for atomic model fitting into EM data.
  • It enhances the ability to interpret macromolecular structures at near-atomic resolution.
  • The tool is freely available and applicable to diverse structural biology problems.