Anders J. Markvardsen

Mantid—Data analysis and visualization package for neutron scattering and μ SR experiments

The Mantid framework is a software solution developed for the analysis and visualization of neutron scattering and muon spin measurements. The framework is jointly developed by software engineers and scientists at the ISIS Neutron and Muon Facility and the Oak Ridge National Laboratory. The objectives, functionality and novel design aspects of Mantid are described.

A probabilistic approach to space-group determination from powder diffraction data

An algorithm for the determination of the space-group symmetry of a crystal from powder diffraction data, based upon probability theory, is described. Specifically, the relative probabilities of different extinction symbols are assessed within a particular crystal system. In general, only a small number of extinction symbols are relatively highly probable and a single extinction symbol is often significantly more probable than any other. Several examples are presented to illustrate this approach.

A hybrid Monte Carlo method for crystal structure determination from powder diffraction data

A hybrid Monte Carlo algorithm for crystal structure determination from powder diffraction data is presented. The algorithm combines the key components of molecular dynamics and Monte Carlo simulations to achieve efficient sampling of phase space, allowing the crystal structure of capsaicin to be determined from powder diffraction data more effectively than by a simulated-annealing approach. The implementation of the algorithm, the choice of the simulation parameters and the performance of the algorithm are discussed.

Powder diffraction based structural studies of pharmaceuticals

Abstract Recent methodological and algorithmic developments in the field of structure determination of materials of pharmaceutical interest from powder diffraction data are discussed.

A maximum-likelihood method for global-optimization-based structure determination from powder diffraction data.

A maximum-likelihood algorithm has been incorporated into a crystal structure determination from a powder diffraction data framework that uses an integrated-intensity-based global optimization technique. The algorithm is appropriate when the structural model being optimized is not a complete description of the crystal structure under study.

Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data

Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo integration, which provides the full diffraction intensities. However, apart from having to perform this merging, the Monte Carlo integration must also average out all variations in crystal quality, crystal size, X-ray beam properties and other factors, necessitating data collection from thousands of crystals. Because the pulses provided by FELs running in the typical self-amplified spontaneous emission (SASE) mode of operation have very irregular, spiky spectra that vary strongly from pulse to pulse, it has been suggested that this is an important source of variation contributing to inaccuracies in the intensities, and that, by using monochromatic pulses produced through a process called self-seeding, fewer images might be needed for Monte Carlo integration to converge, resulting in more accurate data. This paper reports the results of two experiments performed at the Linac Coherent Light Source in which data collected in both SASE and self-seeded mode were compared. Importantly, no improvement attributable to the use of self-seeding was detected. In addition, other possible sources of variation that affect SFX data quality were investigated, such as crystal-to-crystal variations reflected in the unit-cell parameters; however, these factors were found to have no influence on data quality either. Possibly, there is another source of variation as yet undetected that affects SFX data quality much more than any of the factors investigated here.

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

The structure determination of P-type ATPase–ligand complexes from microcrystals by serial femtosecond crystallography using a free-electron laser is described. The feasibility of the method for ligand screening is demonstrated, and SFX data quality metrics as well as suitable refinement procedures are discussed.

ExtSym: a program to aid space‐group determination from powder diffraction data

Once unit-cell dimensions have been determined from a powder diffraction data set and therefore the crystal system is known (e.g. orthorhombic), the method presented by Markvardsen, David, Johnson & Shankland [Acta Cryst. (2001), A57, 47-54] can be used to generate a table ranking the extinction symbols of the given crystal system according to probability. Markvardsen et al. tested a computer program (ExtSym) implementing the method against Pawley refinement outputs generated using the TF12LS program [David, Ibberson & Matthewman (1992). Report RAL-92-032. Rutherford Appleton Laboratory, Chilton, Didcot, Oxon, UK]. Here, it is shown that ExtSym can be used successfully with many well known powder diffraction analysis packages, namely DASH [David, Shankland, van de Streek, Pidcock, Motherwell & Cole (2006). J. Appl. Cryst. 39, 910-915], FullProf [Rodriguez-Carvajal (1993). Physica B, 192, 55-69], GSAS [Larson & Von Dreele (1994). Report LAUR 86-748. Los Alamos National Laboratory, New Mexico, USA], PRODD [Wright (2004). Z. Kristallogr. 219, 1-11] and TOPAS [Coelho (2003). Bruker AXS GmbH, Karlsruhe, Germany]. In addition, a precise description of the optimal input for ExtSym is given to enable other software packages to interface with ExtSym and to allow the improvement/modification of existing interfacing scripts. ExtSym takes as input the powder data in the form of integrated intensities and error estimates for these intensities. The output returned by ExtSym is demonstrated to be strongly dependent on the accuracy of these error estimates and the reason for this is explained. ExtSym is tested against a wide range of data sets, confirming the algorithm to be very successful at ranking the published extinction symbol as the most likely

Characterization of a hybrid Monte Carlo search algorithm for structure determination

A hybrid Monte Carlo (HMC) search algorithm has recently been shown to be a promising method for structure determination from powder diffraction data [Johnston, David, Markvardsen & Shankland (2002). Acta Cryst. A58, 441–447]. Here, the performance of the algorithm on a number of different crystal structures is investigated as a function of its control parameters. This detailed analysis required the use of a system for distributed computing in order to keep the calculation times within a reasonable time frame. The results obtained confirm previous findings and a detailed discussion of the effect of the control parameters on the efficiency of the HMC method is provided. The results suggest a method for setting these parameters automatically, which is an essential step if HMC is to find routine use in the determination of crystal structures.

Conformational analysis by solid-state NMR and its application to restrained structure determination from powder diffraction data

Solid-state NMR is used to dramatically improve the efficiency and reliability of molecular crystal structure determination from X-ray powder diffraction data.