Richard Cooper

May 122011

CRYSTALS v14.23c installer is available to download for the Windows platfom.

[Update – patched version 1423c released 27 May, fixes format problem with tiny weights in FCF, CIF input bug]

Selected highlights:

  • Added bond colouring to indicate either element type, or disordered part
  • Improved robustness of weighting scheme 17 (Shelx weights)
  • Output observation weights in FCF CIF
  • Allow omission of Friedel pairs of reflections from Absolute Configuration plots.
  • Fixed crash on ‘Select All’ atoms for large structures.
  • Fixed Hide/Show H button on toolbar.
Apr 212011

CRYSTALS v14.21 installer is available to download for the Windows platfom.

Selected highlights:

  • Constraints (List 12), restraints (List 16) and manually omitted reflections (List 28) are appended to the CIF for easy reference.
  • Punch for list 1 is now possible.
  • Included slant 2Fo-Fc maps on the menu.
  • Fixed 2 bugs in #Perhydro: phenyl rings now work again and addition of H to disordered components is fixed.
  • New list 9 stores parameter standard uncertainties from last cycle of least squares.
  • New script for reading general CIFs from diffractometers.
  • New script for centering structures in cells.
  • Reduced number of questions during reading back of Superflip solutions.
  • New script for editing f’ and f”.


Mar 302011

Rowena ScottIn-situ Diamond RingNot content with showing off the eye-catching brilliance of her new diamond engagement ring, final year Inorganic Chemistry student Rowena Scott wanted to reveal the beautiful symmetry of its atomic structure. She recorded an X-ray diffraction pattern from the diamond using one of the Chemistry Department’s new state of the art, SuperNova dual source X‑ray diffractometers.

Rowena’s current research project with Dr Simon Clarke involves the synthesis of iron chalcogenide superconductors. The structures of these materials are then determined using single crystal X-ray diffraction techniques.

Chemical Crystallography Service manager, Dr Amber Thompson said “We see a wide range of materials of varying crystallinity from many research groups in the Department of Chemistry, usually grown at the bottom of glass schlenks or flasks; it’s not often that such a lovely crystal turns up mounted in a band of gold”.

Diffraction pattern of the diamondThe diffracted X-rays were measured while rotating the diamond in an X-ray beam. The resulting diffraction pattern shows the position and intensity of the beams diffracted by the organised structure of carbon atoms in the crystal. The white rings overlaid on the image indicate the angles at which diamond peaks are expected to occur, which agree with the collected data.

Diamond diffracts X-rays so efficiently that the X-ray generator had to be run at 10% of its usual power in order to avoid overloading the X-ray detector.

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.

Electronic reprints

Publisher’s copy

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.

Publishers copy:

Nov 172010

Jeremy Law, a Part II student working with Dr Nick Rees and Dr David Watkin, has won a prize for his poster entitled “Alternative Approaches to Hydrogen Atom Location in the Solid State”. He presented his work to the joint ISIS Crystallography User Group and British Crystallographic Association PCG/SCMP meeting “Current Research in Physical Crystallography”

Nov 162010

Congratulations to Dr David Watkin who received an award under the Oxford Teaching Awards scheme for excellence in teaching as attested by student feedback and with the support of the department. He received a certificate presented by Professor Andrew Hamilton, the Vice-Chancellor of Oxford at Rhodes House.
The Oxford Teaching Awards scheme, co-ordinated by the Oxford University Learning Institute, recognises outstanding contributions award winners have made to teaching and learning at Oxford.

Jul 312010

CRYSTALS v14.11 is available as a beta-test.

Many small changes in Regularise Replace thanks to a CRYSTALS workshop in Toulouse organised by Carine Duhayon and Laure Vendier.

Cif generator now properly includes esds on refined hydrogen bonds, has incrreased figure-fields for cell parameters, and appends constraint and restraint information as _iucr_ data items at end of cif.

Improved scaling of difference Pattersons – see forthcoming paper by Flack, Sadki, Thompson & Watkin.

Absolute configuration routine (based on PLATON with Ton Spek’s permission) extended to provide more diagnostics and additional data to be re-input as absolute-structure strengthening restraints (see paper by Flack et al. above).

Error tracking for “USE” files has been improved.

Collaboration with Ernesto Mesto (Dipartimento Geomineralogico – Università degli Studi di Bari) uncovered over-sights in the original 1979 code, which lost contributions when a twin component fell onto a centring absence. Difference maps with twinned data now seem to reveal hydrogen atoms very reliably.

Jul 132010

Cryst. Rev. (2010), 16(3), 197-230.    [ doi:10.1080/08893110903483246 ]

X-ray single crystal structure analysis has become a gold standard for the determination of molecular geometry. The reliability of the technique is a triumph for science and technology working together. The uniqueness of well-crystalline material intrigued early natural philosophers, and their examinations, followed by the discovery of the diffraction of X-rays by crystals, led to the powerful technology that we now enjoy. For about three quarters of a century molecular structure determination has been a driving force for crystallographic research, but now that the science has matured into a technology, interest is returning in trying to understand the nature of crystals themselves.