SMTK – a small-molecule toolkit library for crystallographic modelling and refinement

Abstract

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.

Practical applications of averages and differences of Friedel opposites

“…However, on increasing the value of k above 1, the weight of the Friedel-difference intensities becomes larger and their influence increases. However, with SMTK, the Small Molecule Tool Kit (Sadki & Watkin, 2011), it is possible to minimize the S of equation (10) for different values of k. In this way refinements were undertaken on the compounds WIGWUF, XICNED and SIHDET for a large range of values of k. In fact, the data for the refinements included only the paired acentric reflections whilst the centric and unpaired acentric reflections were omitted. However, with SMTK, the Small Molecule Tool Kit (Sadki & Watkin, 2011), it is possible to minimize the S of equation (10) for different values of k. In this way refinements were undertaken on the compounds WIGWUF, XICNED and SIHDET for a large range of values of k. In fact, the data for the refinements included only the paired acentric reflections whilst the centric and unpaired acentric reflections were omitted.…”

“…As examples, the A obs -, A model -and (A obs À A model )-Pattersons have been calculated with SMTK (Sadki & Watkin, 2011) for the compounds XICNED and DOPKID (Harvey et al, 2009) using only the measurements of A(hkl). For XICNED, at least the first 20 highest peaks of the A obs -and A model -Pattersons are approximately at the same position with the same intensity (peak Q1 at the origin has heights of 5267 and 5241; peak Q2 has heights of 480 and 478; and peak Q18 has heights of 328 and 330, respectively).…”

“…It is not possible to undertake least-squares refinement to minimize the S in equation (10) with conventional crystallographic software. However, with SMTK, the Small Molecule Tool Kit (Sadki & Watkin, 2011), it is possible to minimize the S of equation (10) for different values of k. In this way refinements were undertaken on the compounds WIGWUF, XICNED and SIHDET for a large range of values of k. In fact, the data for the refinements included only the paired acentric reflections whilst the centric and unpaired acentric reflections were omitted. The results are given in Table 2.…”