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Related Concept Videos

X-ray Crystallography02:18

X-ray Crystallography

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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...
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X-ray Diffraction of Biological Samples01:10

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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...
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Updated: Jan 6, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

Dorothee Liebschner1, Pavel V Afonine1, Matthew L Baker2

  • 1Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Acta Crystallographica. Section D, Structural Biology
|October 8, 2019
PubMed
Summary

Phenix software aids in determining macromolecular structures using diffraction and cryo-electron microscopy. It automates workflows for data processing, model building, and refinement, accelerating biological discovery and therapeutic development.

Keywords:
C++PhenixPythonX-raysautomationcctbxcryo-EMdiffractionmacromolecular crystallographyneutrons

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Macromolecular structures are crucial for understanding biological mechanisms and developing therapeutics.
  • Techniques like X-ray diffraction and cryo-electron microscopy provide essential structural data.
  • Method-specific data properties necessitate tailored software for accurate structure determination.

Purpose of the Study:

  • To introduce Phenix, a versatile software package for macromolecular structure determination.
  • To highlight Phenix's capability to handle data from various diffraction and microscopy techniques.
  • To emphasize Phenix's focus on automation and best practices in structure solution.

Main Methods:

  • Phenix integrates tools for data quality assessment, map improvement, and model building.
  • It supports the entire structure determination cycle, including validation, rebuilding, and refinement.
  • The software accommodates data from X-ray, neutron, electron diffraction, and cryo-electron microscopy.

Main Results:

  • Phenix offers method-specific tools catering to the unique properties of different experimental data.
  • Automation of repetitive tasks minimizes manual effort and enhances efficiency.
  • A graphical user interface simplifies access to command-line features and project management.

Conclusions:

  • Phenix provides a comprehensive and adaptable platform for macromolecular structure determination.
  • Its automated features and user-friendly interface streamline the structure solution workflow.
  • The software facilitates advancements in biological research and drug discovery by enabling efficient structure determination.