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.

Publisher’s copy: IUCr

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.

The Absolute Configuration of 1-Epialexine Hemihydrate

Dec 152008
 

Acta Cryst. (2008), C64, o649-o652.    [ doi:10.1107/S0108270108037086 ]

The absolute and relative configurations of 1-epialexine are established by X-ray crystallographic analysis, giving (1S,2R,3R,7S,7aS)-1,2,7-trihydroxy-3-(hydroxymethyl)pyrrolizidine. The compound crystallizes as the hemihydrate C8H15NO4·0.5H2O, with hydrogen bonds holding the water molecule in a hydrophilic pocket between epialexine bilayers. In addition, a comparison was made between results obtained from examination of the Bijvoet pairs from data sets collected using molybdenum and copper radiation.

Structure Refinement: Some Background Theory and Practical Strategies

May 152008
 

J. Appl. Cryst. (2008), 41, 491-522.    [ doi:10.1107/S0021889808007279 ]

Most modern small-molecule refinement programs are based on similar algorithms. Details of these methods are scattered through the literature, sometimes in books that are no longer in print and usually in mathematical detail that makes them unattractive to nonprogrammers. This paper aims to discuss these well established algorithms in nonmathematical language, with the intention of enabling crystallographers to use their favourite programs effectively.

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

CRYSTALS Enhancements: Refinement of Atoms Continuously Disordered Along a Line, on a Ring or on the Surface of a Sphere

Apr 222004
 

J. Appl. Cryst. (2004), 37, 545-550.    [ doi:10.1107/S0021889804009847 ]

A Cp* fragment consisting of partial atoms embedded in annuliThe program CRYSTALS [Betteridge, Carruthers, Cooper, Prout & Watkin (2003). J. Appl. Cryst. 36, 1487] has been extended to include an option for the refinement of a continuous electron density distribution lying along a line, a ring or on the surface of a sphere. These additional non-atomic electron distributions can be refined in any combination with traditional anisotropically distributed spherical atoms, including the refinement of `partial’ atoms overlapping with the special electron distributions.

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CRYSTALS Version 12: Software for Guided Crystal Structure Analysis

Dec 012003
 

J. Appl. Cryst. (2003), 36, 1487.    [ doi:10.1107/S0021889803021800 ]

CRYSTALS version 12 contains a modern crystallographic user interface, and novel strategies that incorporate chemical knowledge and crystallographic guidance into the crystal structure analysis software.

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