Citations
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Journal ArticleDOI
Scaling and assessment of data quality
TL;DR: The various physical factors affecting measured diffraction intensities are discussed, as are the scaling models which may be used to put the data on a consistent scale and algorithms used by the CCP4 scaling program SCALA.
Journal ArticleDOI
PHENIX: building new software for automated crystallographic structure determination
Paul D. Adams,Ralf W. Grosse-Kunstleve,Li-Wei Hung,Thomas R. Ioerger,Airlie J. McCoy,Nigel W. Moriarty,Randy J. Read,James C. Sacchettini,Nicholas K. Sauter,Thomas C. Terwilliger +9 more
TL;DR: 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.
Journal ArticleDOI
VESTA: a three-dimensional visualization system for electronic and structural analysis
Koichi Momma,Fujio Izumi +1 more
TL;DR: VESTA as mentioned in this paper is a cross-platform program for visualizing both structural and volumetric data in multiple windows with tabs, including isosurfaces, bird's-eye views and two-dimensional maps.
Journal ArticleDOI
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
E. Krissinel,Kim Henrick +1 more
TL;DR: The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.
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How good are my data and what is the resolution
TL;DR: The new scaling program AIMLESS is described and tests of refinements at different resolutions are compared with analyses from the scaling step.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Crystal structure refinement with SHELXL
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Journal ArticleDOI
Coot: model-building tools for molecular graphics.
Paul Emsley,Kevin Cowtan +1 more
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Journal ArticleDOI
Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.