Practical Applications of Averages and Differences of Friedel Opposites

Dec 072010
 

Acta Cryst. (2011), A67, 21-34.    [ doi:10.1107/S010876731004287X ]

The practical use of the average and difference intensities of Friedel opposites at different stages of structure analysis has been investigated. It is shown how these values may be properly and practically used at the stage of space-group determination. At the stage of least-squares refinement, it is shown that increasing the weight of the difference intensities does not improve their fit to the model. The correct form of the coefficients for a difference electron-density calculation is given. In the process of structure validation, it is further shown that plots of the observed and model difference intensities provide an objective method to evaluate the fit of the data to the model and to reveal insufficiencies in the intensity measurements. As a further tool for the validation of structure determinations, the use of the Patterson functions of the average and difference intensities has been investigated and their clear advantage demonstrated.

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SMTK - A Small-Molecule Toolkit Library for Crystallographic Modelling and Refinement

Nov 272010
 

J. Appl. Cryst. (2011), 44, 52-59.    [ doi:10.1107/S0021889810042470 ]

One of the requirements for the next generation of small-molecule crystallographers is a mathematical programming infrastructure. It should provide a modelling design process, where the model formulation is kept separate from the optimization process to provide gains in reliability, scalability and extensibility, enabling the application of optimization components in general, and refinement-based applications in particular, as applied to crystallographic problems. A research project has been undertaken to design and implement an innovative toolkit library – a small-molecule toolkit (SMTK) – for crystallographic modelling and refinement. This paper provides an overview of SMTK and its object-oriented implementation. As a practical illustration, it also shows the context of use for a set of classes and discusses how the toolkit enables the user rapidly to develop, maintain and explore the full capabilities of crystallography and so create new applications. SMTK reduces the degree of effort required to construct and develop new algorithms and provides users with an easy and efficient means to test ideas, as well as to build large and maintainable models which can readily be adapted to any new situation.

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ECM 25

Aug 212009
 

The 25th European Crystallographic Meeting was held in the Harbiye Museum and Cultural Centre in the beautiful city of Istanbul.  It was a very eventful week, and contributions to the conference made by Chem. Cryst. include:

N. David Brown, James Haestier, Mustapha Sadki, Amber L. Thompson & David J. Watkin
A Further Improved Structure Matching Algorithm (Poster)

James Haestier
Handling of Cell Errors and their Effect on Derived Parameters (Poster)

Mustapha Sadki
New Modelling for Disordered Atoms in Free-form Based Hybrid Refinement and Visual Representation (Poster)

Mustapha Sadki
The Application of Novel Modelling and Refinement Strategies to Crystallography (Presentation)

Amber L. Thompson & David J. Watkin
Absolute Configuration Determination – Is there More Information in the Data? (Poster)

David J. Watkin, Richard I. Cooper & Amber L. Thompson
CRYSTALS:  Refinement and Validation Tools (Poster)

David Watkin
The Future of Small Molecule Software (Session Chair)

Handling Cell-Parameter Errors in Crystallographic Data

Aug 012009
 

J. Appl. Cryst. (2009), 42, 798-809.    [ doi:10.1107/S0021889809024376 ]

A new method is presented for handling errors on crystallographic data. In single-crystal diffraction experiments, two variance-covariance matrices are present, one for the cell parameters and the second for the refined parameters (atomic coordinates and anisotropic displacement parameters). These two matrices can be combined so that errors on derived parameters, such as bond distances, bond angles and TLS tensors, may be calculated more simply. The new method works for all space groups but there are limitations on its application to triclinic space groups. The method allows errors to be transformed between space groups.

Publisher copy: IUCr

Error Estimates on Bond-length and Angle Corrections from TLS Analysis

Apr 082008
 

J. Appl. Cryst. (2008), 41, 531-536.    [ doi:10.1107/S0021889808005463 ]

Librational motion within a crystal structure distorts the measured bond distances and angles from their physical values. TLS analysis of a rigid molecule or a rigid part of a molecule allows the calculation of bond-length and angle corrections. Until now, no estimate of the error on these corrections has been available. A method is presented for propagating the errors on the anisotropic displacement parameters (ADPs) to the bond-length and angle corrections which are a function of the libration tensor. The numerical significance of approximations made during the calculation is discussed.

Publisher copy: IUCr

BCA Spring Meeting 2008

Apr 012008
 

The Annual Meeting of the British Crystallography Association was held in York.  Contributions from Chem. Cryst. included:

Anna Collins, Richard I. Cooper, Andrew R. Cowley, David J. Watkin
2-(1-Hydroxy-2-methyl-propyl)-2,5-dihydro-furan-2-carboxylic acid diisopropylamide:  A study of a phase transition to a pseudosymmetrical Z′=2 structure (Poster)

James Haestier, Mustapha. Sadki, Amber L. Thompson and David J. Watkin
Cell Parameter Standard Uncertainties and their Effect on Crystallographic Data (Poster)

Mustapha Sadki, James Haestier, Amber L. Thompson & David J. Watkin
Computational Infrastructure for Bridging the Gap between Previous and Future Generations of Crystallographers (Poster)