Application of Modern Techniques in Crystallographic Software Development

Abstract

This thesis describes contributions made as part of the EPSRC-funded project Age Concern: Crystallographic Software for the Future. Work has been done in various areas of small molecule crystallographic soft- ware development, both within the smtbx (Small Molecule Toolbox) and the Olex2 software.
Chapter 2 details the work that was done towards the smtbx-based re- finement that was developed as part of the “Age Concern” project. A framework was created enabling the inclusion of observations of restraint in the refinement, and new restraints on geometry and anisotropic displacement parameters were added. Refinement of (pseudo-)merohedrally twinned structures was implemented.
In Chapter 3 a description of the determination of absolute structure by various methods is given. The methods of Hooft et al. [2008] and Flack [1983] have been implemented, and a quantitative comparison made between the two methods.
Chapter 4 discusses the method of van der Sluis and Spek [1990] for the refinement of structures containing severely disordered regions. This method has been implemented and a modification designed to give improved results when one or more low angle reflections are missing is proposed and tested, and shown to be beneficial.
Chapter 5 introduces a new module, iotbx.cif, which has been added to the cctbx (Computational Crystallography Toolbox), providing a comprehensive set of tools for the manipulation of Crystallographic Information Files (CIFs).