CRYSTALS Enhancements: Asymmetric Restraints

Sep 212012
 

J. Appl. Cryst. (2012). 45, 1057–1060. [ doi:10.1107/S0021889812035790 ]

The traditional Waser distance restraint, the rigid-bond restraint and atomic displacement parameter (ADP) similarity restraints have an equal influence on both atoms involved in the restraint. This may be inappropriate in cases where it can reasonably be expected that the precision of the determination of the positional parameters and ADPs is not equal, e.g. towards the extremities of a librating structure or where one atom is a significantly stronger scatterer than the other. In these cases, the traditional restraint feeds information from the poorly defined atom to the better defined atom, with the possibility that its characteristics become degraded. The modified restraint described here feeds information from the better defined atom to the more poorly defined atom with minimal feedback.

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Applications of Leverage Analysis in Structure Refinement

Apr 302012
 

J Appl. Cryst. (2012), 45, 417-429. [ doi:10.1107/S0021889812015191 ]

Leverages measure the influence that observations (intensity data and restraints) have on the fit obtained in crystal structure refinement. Further analysis enables the influence that observations have on specific parameters to be measured. The results of leverage analyses are discussed in the context of the amino acid alanine and an incomplete high-pressure data set of the complex bis(salicylaldoximato)copper(II). Leverage analysis can reveal situations where weak data are influential and allows an assessment of the influence of restraints. Analysis of the high-pressure refinement of the copper complex shows that the influence of the highest-leverage intensity observations increases when completeness is reduced, but low leverages stay low. The influence of restraints, notably those applying the Hirshfeld rigid-bond criterion, also increases dramatically. In alanine the precision of the Flack parameter is determined by medium-resolution data with moderate intensities. The results of a leverage analysis can be incorporated into a weighting scheme designed to optimize the precision of a selected parameter. This was applied to absolute structure refinement of light-atom crystal structures. The standard uncertainty of the Flack parameter could be reduced to around 0.1 even for a hydrocarbon.

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CRYSTALS Enhancements: Absolute Structure Determination

Sep 132011
 

J. Appl. Cryst.  (2011), 44, 1017-1022.    [ doi:10.1107/S0021889811034066 ]

A summary of the features for investigating absolute structure available in the crystallographic refinement program CRYSTALS is presented, together with the results of analyses of 150 light-atom structures collected with molybdenum radiation carried out with these tools. The results confirm that the Flack and Hooft parameters are strongly indicative, even when the standard uncertainties are large compared to the thresholds recommended by Flack & Bernardinelli [J. Appl. Cryst. (2000), 33, 1143–1148].

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  • Oxford University Research Archive [direct pdf]

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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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CRYSTALS Enhancements: Dealing with Hydrogen Atoms in Refinement

Jun 292010
 

J. Appl. Cryst. (2010), 43, 1100-1107.    [ doi:10.1107/S0021889810025598 ]

Because they scatter X-rays weakly, H atoms are often abused or neglected during structure refinement. The reasons why the H atoms should be included in the refinement and some of the consequences of mistreatment are discussed along with selected real examples demonstrating some of the features for hydrogen treatment that can be found in the software suite CRYSTALS.

Hydrogen addition in CRYSTALS

Hydrogen addition in CRYSTALS

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BCA Spring Meeting 2010

Apr 152010
 
Susan Huth presents Kirsten Christensen with the Durward Cruickshank Award

Susan Huth presents Kirsten Christensen with the Durward Cruickshank Award

The final dinner of the British Crystallographic Association Spring Meeting in Warwick was interrupted, as always, with the prize winning awards. Amber Thompson was awarded the International Union of Crystallography Prize (a copy of International Tables) for her explanation of the advantages of choosing non-standard space groups. Kirsten Christensen was awarded the Durward Cruickshank prize for a young crystallographer who had made an outstanding contribution to crystallography.

 

 

Other contributions include:

N. David Brown, James Haestier, Mustapha Sadki, Amber L. Thompson & David J. Watkin
matchbOx:  Automatic Structure Matching to Facilitate Crystallographic Refinement (YC Presentation)

Kirsten E. Christensen, Christopher J. Serpell, Nicholas E. Evans & Paul D. Beer
Pushing the Boundaries of Small Molecule Crystallography:  The Challenging Structure of a Macrocyclic Anion Sensor (Poster)

Richard I. Cooper, Amber L. Thompson & David J. Watkin
The Hydrogen Challenge:  Where are we Now? (Poster)

Christopher J. Serpell & Paul D. Beer
Refinement of Large Supramolecular Structures (Presentation)

David J. Watkin
Dealing with Difficult Data (Session Chair)

 

An Unusual Methylene Aziridine Refined in P21/c and the Nonstandard Setting P21/n

Nov 182009
 

Acta Cryst. (2009), C65, o635-o638.    [ doi:10.1107/S0108270109046952 ]

The unusual methylene aziridine 6-tert-butyl-3-oxa-2-thia-1-azabicyclo[5.1.0]oct-6-ene 2,2-dioxide, C9H15NO3S, was found to crystallize with two molecules in the asymmetric unit. The structure was solved in both the approximately orthogonal and the oblique settings of space group No. 14, viz. P21/n and P21/c, respectively. A comparison of these results clearly displayed an increase in the correlation between coordinates in the ac plane for the oblique cell. The increase in the corresponding covariances makes a significant contribution to the standard uncertainties of derived parameters, e.g. bond lengths. Since there is yet no CIF definition for the full variance-covariance matrix, there are clear advantages to reporting the structure in the nonstandard space-group setting.

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David Watkin gives the Kathleen Lonsdale Lecture

Apr 012009
 
David Watkin gives the Lonsdale Lecture

David Watkin gives the Lonsdale Lecture

Every two years, the Young Crystallographers Group of the British Crystallographic Association nominate a speaker to give the prestigious Kathleen Lonsdale Lecture. Traditionally, they invite well respected scientist who has a good rapport with students. This year the Lonsdale Lecturer was David Watkin who is well known within the community, principally as a result of his involvement with the highly respected refinement software CRYSTALS, developed in Oxford and through the BCA biannual teaching school which he co-founded twenty-five years ago.

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