Journal of Applied Crystallography
0021-8898
1600-5767
Anh Quốc
Cơ quản chủ quản: International Union of Crystallography , INT UNION CRYSTALLOGRAPHY
Lĩnh vực:
Biochemistry, Genetics and Molecular Biology (miscellaneous)
Các bài báo tiêu biểu
<i>OLEX2</i>: a complete structure solution, refinement and analysis program New software,OLEX2 , has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis.OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.
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PROCHECK: a program to check the stereochemical quality of protein structures
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<i>ORTEP</i>-3 for Windows - a version of<i>ORTEP</i>-III with a Graphical User Interface (GUI)
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<i>Phaser</i>crystallographic software Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented inPhaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations betweenF + andF − , give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use meanF and anomalous differences ΔF . One of the design concepts ofPhaser was that it be capable of a high degree of automation. To this end,Phaser (written in C++) can be called directly from Python, although it can also be called using traditionalCCP4 keyword-style input.Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
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<i>WinGX</i>suite for small-molecule single-crystal crystallography
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<i>VESTA 3</i>for three-dimensional visualization of crystal, volumetric and morphology data VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version,VESTA 3 , implementing new features including drawing the external morphology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices.
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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
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Single-crystal structure validation with the program<i>PLATON</i> The results of a single-crystal structure determination when in CIF format can now be validated routinely by automatic procedures. In this way, many errors in published papers can be avoided. The validation software generates a set of ALERTS detailing issues to be addressed by the experimenter, author, referee and publication journal. Validation was pioneered by the IUCr journalActa Crystallographica Section C and is currently standard procedure for structures submitted for publication in all IUCr journals. The implementation of validation procedures by other journals is in progress. This paper describes the concepts of validation and the classes of checks that are carried out by the programPLATON as part of the IUCrcheckCIF facility.PLATON validation can be run at any stage of the structure refinement, independent of the structure determination package used, and is recommended for use as a routine tool during or at least at the completion of every structure determination. Two examples are discussed where proper validation procedures could have avoided the publication of incorrect structures that had serious consequences for the chemistry involved.
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<i>WinGX</i>and<i>ORTEP for Windows</i>: an update TheWinGX 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. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as theSIR andSHELX suites of programs. The programORTEP for Windows provides a graphical user interface (GUI) for the classicORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programsWinGX andORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.
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