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PHENIX: a comprehensive Python-based system for macromolecular structure solution
  • P. Adams, P. Afonine, +15 authors P. Zwart
  • Computer Science, Medicine
  • Acta crystallographica. Section D, Biological…
  • 22 January 2010
The PHENIX software for macromolecular structure determination is described and its uses and benefits are described. Expand
Crystallography & NMR system: A new software suite for macromolecular structure determination.
The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. Expand
Phaser crystallographic software
A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
PHENIX: building new software for automated crystallographic structure determination.
A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is developed, which will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer. Expand
Towards automated crystallographic structure refinement with phenix.refine
This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods. Expand
Structural Basis for Double-Stranded RNA Processing by Dicer
The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA substrates into small fragments about 25 nucleotides in length and itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end. Expand
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
The highly automated PHENIX AutoBuild wizard is described. The procedure can be applied equally well to phases derived from isomorphous/anomalous and molecular-replacement methods.
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
Ten measures of experimental electron-density-map quality are examined and the skewness of electron density is found to be the best indicator of actual map quality. A Bayesian approach to estimatingExpand
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X-rays, neutrons and electrons.
SPARX, a new environment for Cryo-EM image processing.
SPARX (single particle analysis for resolution extension) is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. ItExpand