Age Concern: Crystallographic Software for the Future
Lead Research Organisation:
University of Oxford
Department Name: Oxford Chemistry
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Organisations
Publications
Bourhis L
(2006)
Small molecule crystallography for the future
in Acta Crystallographica Section A Foundations of Crystallography
Brown N
(2009)
A further improved structure-matching algorithm
in Acta Crystallographica Section A Foundations of Crystallography
Cooper R
(2010)
CRYSTALS enhancements: dealing with hydrogen atoms in refinement
in Journal of Applied Crystallography
Flack HD
(2011)
Practical applications of averages and differences of Friedel opposites.
in Acta crystallographica. Section A, Foundations of crystallography
Haestier J
(2009)
Handling cell-parameter errors in crystallographic data
in Journal of Applied Crystallography
Haestier J
(2010)
Handling cell errors in crystallographic data
in Crystallography Reviews
Haestier J
(2008)
Error estimates on bond-length and angle corrections from TLS analysis
in Journal of Applied Crystallography
Haestier J
(2009)
Handling of cell errors and their effect on derived parameters
in Acta Crystallographica Section A Foundations of Crystallography
Sadki M
(2010)
SMTK - a small-molecule toolkit library for crystallographic modelling and refinement
in Journal of Applied Crystallography
Sadki M
(2006)
Open Source software for small molecule crystallography
in Acta Crystallographica Section A Foundations of Crystallography
| Description | Structure Refinement Conventional refinement programs offer the user a selection of pre-programmed options for dealing with foreseen problems. We have taken the opportunity to break with this tradition and offer the next generation of small-molecule crystallographers a totally original crystallography-orientated mathematical programming infrastructure. We have designed a small-molecule toolkit, now in the testing phase, (SMTK, Sadki & Watkin, 2011) for crystallographic modelling and refinement. It provides an environment where the model formulation is kept separate from the optimization process. This provides users with an effective means to test ideas through tools which enable them to develop, maintain and explore new domains of crystallography without the burden of designing the optimisation process. SMTK reduces the effort required to explore new algorithms and to build large and maintainable models which can readily be adapted to any new situation. In building the tool kit use was made of cctbx for routine crystallographic operation. Bespoke code was written to perform in-house optimisations, but the problems can also be packaged up for export to a variety of non-conventional web-based optimisation engines. The advantage of this is that users faced with unstable or otherwise difficult problems have access to the latest mathematical technology. These technologies include automatic redundant parameter elimination, inequality (boundary) constraints and acceleration of sparse matrix operations. The program has been tested by comparing the results of the built-in optimiser with those from external optimisers and with existing refinement programs. Novel uses for it include robust determination of absolute configuration (Flack, Sadki, Thompson & Watkin, 2011), improved joint refinement of X-ray and neutron data (in preparation) and the modelling of disorder using hindered rotors (in preparation). Simplified or partial implementation of some of the ideas explored in SMTK have been back-ported into CRYSTALS as part of the validation procedure and offer existing users a glimpse of what is possible with the tool kit. Using Chemical Information The empirical or approximate molecular formula is usually available at the start of most X-ray analyses of molecular materials. Often, the chemist also has a good idea of the structural formula. Before the start of this project there was no software which attempted to use this knowledge. The program MatchbOx uses the structural information encoded as a SMILES string to automate some of the decision-making steps usually made by a human analyst. The work has involved implementing existing graph-matching algorithms and then extending them to exploit chemical connectivity. This enables the program to detect incorrect atom assignments and to analyse disorder. Output from the program includes graphical displays, crystallographic information files (cif) for the corrected structure, and the information needed for the refinement of disorder. For testing purposes the program has been linked to CRYSTALS, but it is also available as a free standing application for use with any other crystallographic systems. Ten papers coming out of this work have been published, three more are in preparation, and 8 oral presentations have been given at international meetings. |
| Exploitation Route | None in the short term, though the design would enable a teaching interface to be developed. Once testing is completed, the Tool Kit will be deposited with the International Union of Crystallography as an open-source resource. This will make it freely available for exploitation to the whole crystallographic community |
| Sectors | Chemicals,Pharmaceuticals and Medical Biotechnology |
| Description | Simplified or partial implementation of some of the ideas explored in SMTK have been back-ported into the CRYSTALS package, and are available for use free of charge in this package. |
| Sector | Chemicals,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Cultural |