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X-ray Crystallography02:18

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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.
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Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
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Crystal Field Theory
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Phasertng: directed acyclic graphs for crystallographic phasing.

Airlie J McCoy1, Duncan H Stockwell1, Massimo D Sammito1

  • 1Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.

Acta Crystallographica. Section D, Structural Biology
|January 6, 2021
PubMed
Summary
This summary is machine-generated.

New crystallographic phasing software, Phasertng, uses directed acyclic graphs to manage structure solution pathways. This modular approach accelerates the exploration and ranking of structural hypotheses for improved phasing strategies.

Keywords:
PhaserPhasertngSAD phasingdirected acyclic graphsmachine learningmaximum likelihoodmolecular replacement

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Area of Science:

  • Structural Biology
  • Computational Crystallography

Background:

  • Crystallographic phasing requires evaluating numerous structural hypotheses.
  • Advancements enable phasing from small fragments and weak experimental data.

Purpose of the Study:

  • To introduce Phasertng, a novel crystallographic software.
  • To demonstrate the utility of directed acyclic graphs in phasing strategies.

Main Methods:

  • Developed Phasertng with a modular codebase emphasizing scripting and speed.
  • Utilized directed acyclic graphs for native input/output.
  • Applied Phasertng.xtricorder for data analysis in phasing.

Main Results:

  • Phasertng facilitates efficient management of phasing pathways.
  • The directed acyclic graph approach generalizes beyond Phasertng.
  • Demonstrated advantages in analyzing data for molecular replacement and experimental phasing.

Conclusions:

  • Directed acyclic graphs offer a generalized framework for crystallographic phasing.
  • Phasertng enhances modularity, speed, and algorithmic development.
  • This approach supports multifaceted searches and machine learning integration for superior phasing strategies.