A short history of SHELX
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TLDR
This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.Abstract:
An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.read more
Citations
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Journal ArticleDOI
Structure validation in chemical crystallography
TL;DR: This paper reports on the current status of structure validation in chemical crystallography and describes the current state of research in this area.
Journal ArticleDOI
Overview of the CCP4 suite and current developments.
Martyn Winn,Charles Ballard,Kevin Cowtan,Eleanor J. Dodson,Paul Emsley,Phil Evans,Ronan M. Keegan,Eugene Krissinel,Andrew G. W. Leslie,Airlie J. McCoy,Stuart McNicholas,Garib N. Murshudov,Navraj S. Pannu,E. Potterton,Harold R. Powell,Randy J. Read,Alexei A. Vagin,Keith S. Wilson +17 more
TL;DR: An overview of the CCP4 software suite for macromolecular crystallography is given.
Journal ArticleDOI
WinGX and ORTEP for Windows: an update
TL;DR: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF.
Journal ArticleDOI
REFMAC5 for the refinement of macromolecular crystal structures
Garib N. Murshudov,Pavol Skubák,Andrey Lebedev,Navraj S. Pannu,Roberto A. Steiner,Robert A. Nicholls,Winn,Fei Long,Alexei A. Vagin +8 more
TL;DR: The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.
Journal ArticleDOI
Towards automated crystallographic structure refinement with phenix.refine
Pavel V. Afonine,Ralf W. Grosse-Kunstleve,Nathaniel Echols,Jeffrey J. Headd,Nigel W. Moriarty,Marat Mustyakimov,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Peter H. Zwart,Paul D. Adams,Paul D. Adams +11 more
TL;DR: 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.
References
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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
Phase annealing in SHELX-90: direct methods for larger structures
TL;DR: In this article, a phase annealing method, related to the simulated-annealing approach in other optimization problems, is proposed and it is shown that it can result in an improvement of up to an order of magnitude in the chances of solving large structures at atomic resolution.
Journal ArticleDOI
On enantiomorph‐polarity estimation
TL;DR: In this article, the behaviour of the Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds.
Journal ArticleDOI
Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
Simon C. Lovell,Ian W. Davis,W. Bryan Arendall,Paul I.W. de Bakker,J. Michael Word,Michael G. Prisant,Jane S. Richardson,David S. Richardson +7 more
TL;DR: Geometrical validation around the Cα is described, with a new Cβ measure and updated Ramachandran plot, and Favored and allowed ϕ,ψ regions are also defined for Pro, pre‐Pro, and Gly (important because Gly ϕ‐ψ angles are more permissive but less accurately determined).