An alphabetically ordered list of software or computational crystallography based websites
If you are aware of a good site or you just want your site to be listed on this page all you need to do is post:
1. the website's URL
2. a brief but accurate description of the site
3. a small logo for your website/company ideally square 64wxXh (with permission to reproduce on our site and host a copy on our servers)
We will then check that the details are correct and if appropriate upload your link.
Why not give it ago?
Website jammed packed with crystallographic code and interesting stuff. ALB stands for Armel Le Bail and since Le Bail fitting is mentioned also every MOF meeting or any place there is a powder pattern in Liverpool Uni Chemistry department I recommend you take a look.
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Avant-garde Materials Simulation SARL (AMS) is privately owned and was created in 2002 in France with funding and strong support from a major pharmaceutical company. The company’s main goal is the development of software for crystal structure prediction (GRACE initiative). In 2006, the GRACE initiative was joined by another major pharmaceutical company.
In 2007 AMS opened a subsidiary, Avant-garde Materials Simulation Deutschland GmbH, in Freiburg, Germany, where all contract research is carried out.
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BayMEM is a computer program for crystallographic applications of the Maximum Entropy Method (MEM). It can be used to derive the electron density in the unit cell from phased x-ray diffraction data. Different types of PRIOR densities are available. Special feature of BayMEM is that it can be used to determine the electron density of incommensurate crystals in the superspace unit cell.
The use of BayMEM is free of charge for academic research.
If you are interested in obtaining a copy of BayMEM please contact Sander van Smaalen at the University of Bayreuth. You will be send a licence agreement, which you will have to sign and return, before you will receive a copy of BayMEM.
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Bilbao Crystallographic Server
The server contains various space group and symmetry tools, including tools for comparing structures.
The Bilbao Crystallographic Server is a web site with crystallographic programs and databases accessible via Internet. Its development has started in 1997 at the Materials Laboratory (which includes the Departments of Condensed Matter Physics and Applied Physics II) at University of Basque Country, Spain.
The programs available on the server do not need a local installation and can be used free of charge. The only requirement is an Internet connection and a web browser. Please cite the Bilbao Crystallographic Server if you use the programs it contains in research.
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The CCDC is a non-profit, charitable institution whose objectives are the general advancement and promotion of the science of chemistry and crystallography for the public benefit. The primary responsibility of the CCDC is the acquisition, evaluation, dissemination and use of the world's output of small molecule crystal structures as the Cambridge Structural Database (CSD). This database system (CSDS) is provided with a range of software for searching, analysing and visualising crystal structure information consisting of ConQuest, Mercury, Vista, IsoStar, Mogul, PreQuest & WebCSD.
Aside from the CSDS, the CCDC has also developed a number of other scientific software packages including:
• GOLD - an accurate and reliable protein-ligand docking program
• Relibase+ - an essential tool for searching, exploring and comparing all protein-ligand data from public and in-house data sources.
• DASH - a program for crystal structure solution from powder diffraction data
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The Collaborative Computational Projects (CCPs) bring together leading UK expertise in key fields of computational research to tackle large-scale scientific software development, maintenance and distribution projects. Each project represents many years of intellectual and financial investment. The aim is to capitalise on this investment by encouraging widespread and long term use of the software, and by fostering new initiatives such as High End Computing consortia.
Of course CCP4 & 14 are already listed
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The CCP14 (Collaborative Computational Project No. 14) in Powder and Small Molecule Single Crystal Diffraction was initiated in 1994 to collect the best and most commonly used programs. The software located on the CCP14 site is freely available to academic users.
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The Collaborative Computational Project Number 4 in Protein Crystallography was set up in 1979 to support collaboration between researchers working on such software in the UK, and to assemble a comprehensive collection of software to satisfy the computational requirements of the relevant UK groups. CCP4 was originally supported by the UK Science and Engineering Research Council (SERC), and is now supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The project is coordinated at STFC Daresbury Laboratory
. The results of this effort gave rise to the CCP4 program suite, which is now distributed to academic and commercial users world-wide.
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The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system. The goal of the PHENIX project is to advance automation of macromolecular structure determination. PHENIX depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications.
To maximize reusability and, maybe even more importantly, to give individual developers a notion of privacy, the cctbx is organized as a set of smaller modules. This is very much like a village (the cctbx project) with individual houses (modules) for each family (groups of developers, of any size including one).
The cctbx code base is available without restrictions and free of charge to all interested developers, both academic and commercial. The entire community is invited to actively participate in the development of the code base. A sophisticated technical infrastructure that enables community based software development is provided by SourceForge. This service is also free of charge and open to the entire world.
The cctbx is designed with an open and flexible architecture to promote extendability and easy incorporation into other software environments. The package is organized as a set of ISO C++ classes with Python bindings. This organization combines the computational efficiency of a strongly typed compiled language with the convenience and flexibility of a dynamically typed scripting language in a strikingly uniform and very maintainable way.
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The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as: computer graphics, scientific visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, mesh generation, numerical methods
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Chemical Database Service
This service gives on-line access to a rich variety of quality databases in the field of chemistry, and the CDS team also provides general support, training and advice. It is free of charge to eligible users. To register you must be affiliated to a University or one of the other academic teaching and research institutions within the UK.
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CrystalExplorer is a fully-featured molecular crystal visualization tool, available for Mac OS X, Windows and Linux. CrystalExplorer provides a new way of visualizing molecular crystals using the full suite of Hirshfeld surface tools.
CrystalExplorer 2.1 is free for academic, non-commercial use.
Currently, CrystalExplorer's mailing list is down so feel free to post to the forum and join the CrystalExplorer group for direct mailing.
Requires a license/registration to run
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The CRYSTALS software package for single crystal X-ray structure refinement and analysis consists of CRYSTALS, Cameron and specially recompiled versions of SIR92 and SHELXS.
SIR and SHELXS provide the direct methods. CRYSTALS and Cameron provide everything else including
* built-in guidance and validation using The GUIDE.
* import and data reduction from many sources: SHELX/XPrep/WinGX format .ins/.hkl files, CAD4 .dat files, KappaCCD import.cif.
* automatic hydrogen atom placement using combined geometric/difference Fourier placement.
* interactive graphical model of the structure
* sophisticated refinement with constraints and restraints
* various reflection weighting schemes
* graphical analysis of data, results and residuals
* refinement of twinned data and discovery of unnoticed twin-laws using the ROTAX procedure
* fourier maps and contour plots. Output to contour, MCE3D, MapView and ASCII formats.
* Acta Cryst friendly CIFS and publication tables
* colour thermal ellipsoid plots in Cameron. Output in WMF, postscript, encapsulated postscript, CHIME formats or print directly to a Windows printer.
* powerful atomic and structural parameter editor
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K., Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487
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Debroglie.net is an essential website for any crystallographer or chemist working in Linux.
It is a repository of add-on packages for Centos 5.x and Fedora 8-11 in crystallography.
Unlike Fedora and other repos it is not tied by stringent licencing rules and is therefore open to academic and other licences.
Installation and update is via yum or direct download from the site. New packages added where possible on request.
Debroglie.net also hosts its own trac
bug report system for tracking bugs in the rpms.
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I will write something proper soon...........
Our research group is interested in methodological improvements and practical aspects of X-ray structure determination and analysis, and in particular in the electron density distribution of solids. Our focus and area of expertise is the inclusion of the non-spherical electron density in structural models of "small-molecule" (up to 1000 atoms) crystal structures. However, it is the discipline of chemistry that provides us with a broader framework of phenomena and questions. One theme uniting the different branches of chemistry, ---organic, biological, medicinal and inorganic--- is structure. X-ray structure analysis is also a playground for the application of computational chemistry, in that it provides real-life examples for study, comparison and verification. Only the mutual exchange of information between experiment and theory enables to distinguish between manifestations of thermal motion and electron density in the solid state. Therefore our studies require the application of advanced computational methodology. Modern computer programs based on quantum mechanics and molecular mechanics are central tools that we use, methods that are complemented by preparational chemistry and crystallisation in the laboratory. Last but not least it is the diffraction experiment itself that X-ray structure analysis is based upon. In order to "measure" the electron density and to derive molecular strucure of a compound of interest each time such an experiment needs to be carried out. Obtaining chemical insight and attempting to arrive at a deeper understanding of the phenomena observed in such experiments is the ultimate motivation for our studies. For more detailed information the reader is refered to our publication list. The work listed there has often involved collaboration partners, and some them are refered to here.
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Eval14 and eval15 are integration methods for single crystal X-ray diffraction on area detectors. Both methods use knowledge about the exact experimental setup.
- Eval14 applies boxsummation (BPB) with predicted reflection boundaries.
- Eval15 applies profile fitting with predicted reflection profiles
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The International Centre for Diffraction Data® (ICDD®) is a non-profit scientific organization dedicated to collecting, editing, publishing, and distributing powder diffraction data for the identification of crystalline materials. The membership of the ICDD consists of worldwide representation from academe, government, and industry.
Thei Vision - The International Centre for Diffraction Data will continue to develop tools and support the education required for materials analyses of tomorrow.
Their Mission - The International Centre for Diffraction Data will continue to be the world center for quality diffraction and related data to meet the needs of the technical community. ICDD promotes the application of materials characterization methods in science and technology by providing forums for the exchange of ideas and information.
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Jana2006 is focused on solution, refinement and interpretation of difficult, especially modulated structures. Input data can be unlimitedly combined, for example powder neutron data with single crystal X-ray data. The structure solution is done using the built-in charge flipping algorithm. Jana can handle multiphase structures (for both powder and single crystal data), merohedric twins, twins with partial overlap, commensurate and composite structures. It contains powerful transformation tools for symmetry (group-subgroup relations), cell parameters and commensurate-supercell relations. Wide scale of constrains and restrains is available including a powerful rigid body approach and possibility to define a local symmetry affecting only part of the structure. The latest development of Jana concerns magnetic structures.
Petricek,V., Dusek,M. & Palatinus,L.(2006). Jana2006. The crystallographic computing system. Institute of Physics, Praha, Czech Republic.
Development of Jana is continuously supported by Grant Agency of the Czech Republic and Academy of Sciences of the Czech Republic.
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A website with almost cult standing for 3D display of mineral structure, plus many more cool features. The site is about 4 years since its last major update but it still does what it was designed to do. Need chime to get the best results. Linux users may get a shock to discover the gnome-chem-utils (yum'able) lets you see the chime images if with a reduced ability.
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Moliso is a program to generate and visualise colour mapped transparent 3D iso-surfaces from experimental XD grid and gaussian cube files.
* Correct transparency mode
* Isosurfaces with adjustable colour gradient
* Atomic displacement ellipsoids (ADP's) with xd.res-/xd.mas- or *cif-files
* Line, point and filling mode
* Easy to control via menu, mouse, keyboard and ini-file
* Easy to create screenshots(*.ppm)
* Easy to create rotating videos (*.avi) in various codecs (vfw)(Windows Version only)
* Experimental resolution independet *.PDF file export
* XD grid files and gaussian cube files can be used
* Constrainable colour gradient
* Sphere maping for pseudo reflection
* Windows and LINUX-versions are avaiable
C.B. Hübschle and P. Luger, J. Appl. Cryst. (2006). 39, 901-904
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Olex2 is a program for the determination, visualisation and analysis of molecular crystal structures. It has a portable, mouse-driven, workflow-oriented and fully comprehensive graphical user interface (GUI).
Olex2 provides the user with a GUI 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 present them in a single, workflow-driven package – with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.
O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann, J. Appl. Cryst. (2009). 42, 339-341
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publCIF takes a crystallographic information file (CIF) and prepares a formatted paper (Preprint) in the style of International Union of Crystallography (IUCr) publications.
The CIF and the Preprint are presented side-by-side and are both editable. Changes made to one are applied to the other as you type.
They have two websites this one:http://journals.iucr.org/services/cif/publcif/
and the one the button on the left links to. One wants an email to download the other doesn't!
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Ok, no body look, I didn't forget to post this link here. Well no one bothered to post a you should put a link to shelx website....
Ok, shelx has become the bread and butter tool for small molecule crystallography work. I won't say exclusively for X-rays as it can be used with neutron data also. I think there are even versions for macromolecules as well. You need to register to get it. Or you can buy it through Bruker. There are versions of the code for all operating systems.
Sheldrick, G.M. (2008). Acta Cryst. A64, 112-122
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This collection contains source code for crystallographic programs that are either no longer actively maintained or have a version archived at a significant point in its historical development. Note that many of them (especially ones with graphic output) will not work without considerable modification to fit the requirements of modern compilers and libraries.
The museum was first created by Armel Le Bail in 1999 (http://sdpd.univ-lemans.fr/museum/
), where it was subsequently found a useful resource by a number of software developers wishing to peruse old code and ideas. It was transferred to the IUCr Computing Commission website in January 2010 by Lachlan Cranswick.
Crystallographic source code of any type, style and age (as a zip file) can be submitted for inclusion into the museum by contacting the Chair of the Computing Commission (who is currently: Harry Powell)
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Tonto is a free object based system for computational chemistry.
It can be built directly from source or the rpm installed on Fedora/Centos builds via the debroglie.net repo.
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VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. Some of the novel features of VESTA are listed below.
* Deal with multiple structural models, volumetric data, and crystal morphologies in the same window.
* Support multiple tabs corresponding to files.
* Support multiple windows with more than two tabs in the same process.
* Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
* Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
* Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
* Transparent isosurfaces can be overlap with structural models.
* Isosurface can be colored on the basis of another physical quantity.
* Arithmetic operations among multiple volumetric data files.
* High quality smooth rendering of isosurfaces and sections.
* Export high-resolution graphic images exceeding Video card limitation.
VESTA runs on Windows, Mac OS X, and Linux. It is contributed free of charge for non-commercial users.
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WinGX is a MS-Windows system of programs for solving, refining and analysing single crystal X-ray diffraction data for small molecules. It provides a consistent and user-friendly GUI for some of the best publically available crystallographic programs, and has interfaces to other popular programs such as SHELX-97 and SirWare programs (SIR-97, SIR-2004). Written and maintained by Louis J. Farrugia, often called the guru of GUIs, it is a extreme useful suite for crystallographers. It can be run using wine on Linux systems.
L. J. Farrugia, J. Appl. Cryst. (1999),32, 837-838
Requires a license/registration to run
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It is developed (since 1985) with the aim to create the original combination consisting of the Crystal Structure Database for Minerals, the automatically formed Calculated Powder X-ray Diffraction Standards (CPDS) SubBase and the Applied Program Package using saved information for Powder X-Ray Diffraction and Crystal Chemical Analysis.
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X-ray Absorption Edges
A periodic table allowing you to select an element and see the X-ray absorption edge energies in angstrom (wavelength). It also provides access to the scattering factors for each element. These data files indexed through the table were calculated using the subroutine library by Brennan and Cowan. The values for f' and f" are derived using the theoretical approximation developed by Cromer and Liberman. This theory gives accurate values far from an absorption edge but does not account for the effects of neighboring atoms, which can be very substantial near an absorption edge. Before conducting an anomalous scattering experiment close to an absorption edge it is therefore advisable to determine the actual scattering behaviour of your sample.
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XDS - X-ray Detector Software
X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. For a description of the package, including references go to their website.
XDS can process data images from CCD-, imaging-plate-, multiwire-, and pixel-detectors in a variety of formats (see Supported detectors
). Detector specific Input file templates greatly simplify the use of XDS; they are provided as part of the documentation.
XDS runs under Unix or Linux on a single server or automatically splits its task for concurrent execution by several remote hosts in a networked (NFS) environment where each host may comprise a shared memory multiprocessor system.
XDS is free of charge for non-commercial applications and available here for downloading. Note, that the executables of the package will expire on March 31, 2009. For industrial usage of XDS a license is required (e-mail enquiry: XDS
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This software uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.
Linux, IRIX, max and windows versions available. Well worth a look.
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A web resource for structures with Z' > 1
Structures with Z' > 1 (i.e. more than one molecule in the asymmetric unit) are of intense current interest. As part of an EPSRC funded project, a web site has been developed dedicated to bringing together all the information and publications known about these fascinating systems.
The main feature of the website is an annotated database of structures with Z' > 4, which is updated regularly. Each entry contains the name, chemical formula, journal reference and Cambridge Structural Database (CSD) Refcode (where applicable) in addition to a "Notes" section reporting anything of interest about the packing or composition of the asymmetric unit, as well as links to polymorphs, redeterminations or similar structures. Possible errors in Z' or space group assignment are also highlighted. The structures included in the database are mainly drawn from the CSD however readers with unpublished high Z' structures are also invited to submit their structures for inclusion in the database.
The website also contains a general introduction to the Z' phenomenon as well as a list of useful references concerning all aspects of high Z' structures.
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Fox, 'Free Objects for Crystallography' is a free, open-source program for the ab initio structure determination from powder diffraction.
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The FullProf Suite (for Windows and Linux) is formed by a set of crystallographic programs (FullProf, WinPLOTR, EdPCR, GFourier, etc...) mainly developed for Rietveld analysis (structure profile refinement) of neutron (constant wavelength, time of flight, nuclear and magnetic scattering) or X-ray powder diffraction data collected at constant or variable step in scattering angle 2theta.
The different programs can be run either in stand alone form (from a console window or clicking directly in a shortcut) or from the interfaces WinPLOTR and/or EdPCR.
The programs within the FullProf Suite are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY of being free of internal errors. In no event will the authors (or their institutions) be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the programs (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs). The authors are not responsible for erroneous results obtained with the programs.
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Fityk [fi:tik] is a program for data processing and nonlinear curve fitting.
Although it is primarily used...
by scientists who analyse data from powder diffraction, chromatography, photoluminescence and photoelectron spectroscopy, infrared and Raman spectroscopy, and other experimental techniques,
to fit peaks – bell-shaped functions (Gaussian, Lorentzian, Voigt, Pearson VII, bifurcated Gaussian, EMG, Doniach-Sunjic, etc.),
... the program can be used for any task that requires fitting a curve to 2D (x,y) data.
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Zeo++ is a open source software for performing high-throughput geometry-based analysis of porous materials and their voids.
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