Cod is updating its coordinate archive and the database from the iucr web site on a regular basis. The results of a singlecrystal structure determination when in cif format can now be validated routinely by automatic procedures. Spek rietan2000 schakal homepage sirware shakenbake shelx software from g. Sincris software list international union of crystallography iucr.
The iucr observes the basic policy of nondiscrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the statutes of the international council for science. Vina autodock autodock vina is a new opensource program for drug discovery, molecular docking and virtual screening, offering multicore capability, high performance and enhanced accuracy and ease of use. Hex hex is an interactive protein docking and molecular superposition program. Platon is written by ton spek, and is a versatile crystallographic tool. Users can perform simple and advanced searches based on annotations relating to sequence. International union of crystallography permits systematic downloads of coordinates files published in the iucr journals. K is shown in the relations below for completeness. Draw a structure or a fragment to search in the cod exact match note. List of electron crystallography software for simulation, quantitative analysis and structure solution, arranged in the alphabetical order adt3d unit cell parameter determination and intensity extraction from tomography diffraction data. Freely available crystallographic software for academia overheads supporting the oral talk at the ill powder diffraction workshop, 22nd23rd march, 1999 this document represents the views and opinions of the author. Structure analysis, checking, and validation tools crystals.
The site features images and animations of crystal structures, and the software can be freely downloaded from the site. Platon program for analysis, verification, and display of organic and organometallic crystal structures. Xray crystallography homepage, xray crystallography at the sealy center for structural biology and molecular biophysics, university of texas medical branch at galveston, texas. Whenever possible a reference to a journal, such as the program section of journal of applied crystallography will be made. Structure of sucrose prepared with platon plutonpovray the program platon is designed as a multipurpose crystallographic tool. By contrast, the crystalline state is characterised by a regular arrangement of atoms over large distances. Crystals are therefore anisotropic their properties vary with.
Ccp14 homepage tutorials and examples platon shelx. Xray 85% of atomic structures in pdb were determined by xray crystallography 2. Then you can either use the menu mapsdifference map, or open the platon graphical menu third icon from the left and choose graphicscontourdiff. In this way, many errors in published papers can be avoided. The method was invented by aaron klug, who won the nobel prize in chemistry for this, and his studies on virus structures and transfer rna, in 1982 the first electron crystallographic protein structure to achieve atomic resolution was bacteriorhodopsin in 1990. It can handle multiple histograms including timeofflight and multiple phases. Subsequently, a project checkcif was initiated to validate crystal structure data supplied in.
Validation has since evolved into an easytouse checkcifplaton webbased iucr service. The software comes with a large set of datafiles and can read the xtaldraw datafiles, but it can also read the american mineralogist crystal structure database data files. Platon a versatile crystallographic program implementing a large variety of standard geometrical calculations, tests, utilities, graphics and several filters. University of kentucky xray crystallography facility external. The software packages currently developed at ic are. Extracts powder pattern information from gsas files and outputs the observed, calculated, difference plots and reflection positions in a form that can be used by graphing software. The program platon is designed as a multipurpose crystallographic tool. On the unix version, this includes the system s system for structure solution and refinement that wraps around a variety of software including, shelxs, crunch. Sincris software list international union of crystallography. Xray crystallography homepage, xray crystallography at the sealy center for.
Net dynamic link library used for the interconversion procedure between variable formats of powder xray files. The source code and compiled versions of the program for various other unix platforms are available from the official platon downloadsite. Sincris server for crystallographic information software ccp14 single crystal and powder diffraction software ccp14 resources and. Macromolecular crystallographic software links ccp4 cns phenix eden crystallography coot o macros for o uppsala software factory pymol home page sharp mosflm other useful crystallography links crystallography on os x xray absorption edges the protein data bank pdb molecular movies data base nucleic acid databank international tables ccp4. Visualization for electronic and structural analysis platon. More than 20000 cif files are downloaded at the moment. The library can be used as a reusable component with any.
Complete crystallographic software package for small molecule structures, including data reduction, structure solution and refinement, calculation of derived parameters, realtime interactive graphics, presentation graphics and preparation of text and tables for publication. Introduction to crystallography amorphous solids are homogeneous and isotropic because there is no long range order or periodicity in their internal atomic arrangement. Calidris electron crystallography software carine crystallography chemray crystal designer crystallographica crystal structure determination software diamond dirdif for windows encifer fityk jana2000 mercury visualizer merohedral crystal twinning molecular graphics with povray and swiss pdb viewer ortepiii oscail x platon polyhedron r pluto. Olexsys maintains olex2 for smallmolecule structure analysis shelx programs for the determination of small sm and macromolecular mm crystal structures by single crystal xray and neutron diffraction, and shellx97 manual. If you wish to add some software in this list please send a message to yves. Other crystallographic links dutch crystallographic society. We would like to show you a description here but the site wont allow us. Iucr platon iucr international union of crystallography. Software contents software for crystallography how to use ftp and other internet tools advertisment papers on software in j. Software listings ccp14 available rietveld software postertalks ccp14 methods, problems and solutions sincris. Spek, utrecht university, padualaan 8, 3584 ch utrecht, the netherlands.
Vesta runs on three major platforms, windows, mac os x. Protein crystallography automation and software news. University of kentucky xray crystallography facility. Current versions of the program platon for windows are available from this site. Software listings ccp14 available rietveld software postertalks ccp14 methods, problems and solutions sincris bilbao crystallographic server misc cryst web software refinement packages available alb crystallography home page george l. Sincris software database for crystallography e software database for crystallography for all software described in sincris database you will find.
Sincris database of software for crystallography kplot multipurpose tool for crystal structure visualization and analysis, free download, software available for windows and linux. Singlecrystal structure validation with the program platon. Workshop powder diffraction structure determination and. Use the up button to backtrack to the higher level closer to. Applied crystallography the editor cannot answer to technical questions about software he did not write. The rcsb pdb also provides a variety of tools and resources. Complete crystallographic software package for small molecule. A full manual for platon is available from the platon homepage platon is written by ton spek, and is a versatile crystallographic tool implementing a. Aca service crystallography sig american chemical society nederlandse vereniging voor kristallografie cambridge crystallographic data center platon for mswindows home page dr l. Vesta is a 3d visualization program for structural models and 3d grid data such as electronnuclear densities. For authors publishing in acta crystallographica section e, this page provides details of how to cite commonly used computer programs in addition to the list given below, we recommend that authors use the more complete list of standard computer software references that is incorporated within publcif to ensure that their references are in the correct format for. Platon is a shelx compatible structure viewing and analysis toolkit software package by ton spek that has a wide variety of functionality. Structure analysis, checking, and validation tools. Crystallography simple english wikipedia, the free.
Here is the ins and hkl data for that solution if you would like to attempt to fix the problems you may want to use wingx to generate res and list files too. The validation software generates a set of alerts detailing issues to be addressed by the experimenter, author, referee and publication journal. Collaborative computational project for single crystallography and powder diffraction. For all software described in sincris database you will find. Overview of the content of this document chapter 0 platon general introduction and information chapter 1 platon implementation and menu driven instructions chapter 2 platon. Software suite for the automated determination of macromolecular structures using xray crystallography and other methods. Farrugia, glasgow home of dirdif and crunch ccp14collaborative computational project the shelx homepage the drawxtl homepage drawing polyhedra ps2pdf. Thus the individual lattice vectors have the following definitions. Anaelu is composed of three interconnected applications, corresponding to three crystallographic tasks. Anaelu software package anaelu analytical emulator laue utility has been created for aiding the interpretation of twodimensional xray diffraction patterns produced by textured bulk and nanostructured samples. Spek, utrecht university, padualaan 8, 3584 ch utrecht, the.
Clark xray facility xray software programs and methods in sdpd data conversion. Mueller institute for structural biology at biozentrum basel sergeiv. The homepage the platon homepage gives pointers to all information available on platon. Crystallography, branch of science that deals with discerning the arrangement and bonding of atoms in crystalline solids and with the geometric structure of crystal lattices. Freely available software to assist in solving structures from. Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope tem. The dll is capable of handling the most common file formats binary and ascii.
The pdb archive contains information about experimentallydetermined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwpdb, the rcsb pdb curates and annotates pdb data according to agreed upon standards. Snb solve crystal structures using the shakeandbake algorithm. The american mineralogist crystal structure database.
Xray crystallography 59553 macdonald research group. Pdf structure validation in chemical crystallography. The result of a crystal structure determination has to be supplied as a cifformatted computerreadable file. Many applets about many aspects of crystallography atomic formfactor curves, quasiperiodic tiling, stereograms, lauegrams, fourier transform etc.
A full manual for platon is available from the platon homepage platon is written by ton spek, and is a versatile crystallographic tool implementing a large. The computational crystallography toolbox cctbx is a reusable scientific software library for. Ccp14 methods, problems and solutions sincris bilbao crystallographic server misc cryst web software. In later discussions, k will be assumed to have a value of 1. Classically, the optical properties of crystals were of value in mineralogy and chemistry for the identification of substances. The information tree in available either with the choise webbrowser through the platon homepage or from platon by rightbutton mouse clicks on menu items, assuming that netscape is accessible from within platon. The author has sole responsibility for its contents lachlan m. Scanorient research and education tool for quickly orientating and indexing backreflection physics laue patterns from polaroid films.
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