James Foadi

University of Bath | UB · Department of Mathematical Sciences

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. T...

KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of ref...

In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom soluti...

Cortical force generators connect epithelial polarity sites with astral microtubules, allowing dynein movement to orient the mitotic spindle as astral microtubules depolymerize. Complexes of the LGN and NuMA proteins, fundamental components of force generators, are recruited to the cortex by Gαi-subunits of heterotrimeric G-proteins. They associate...

Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral memb...

The dynamism of proteins is central to their function, and several proteins have been described as flexible, as consisting of multiple domains joined by flexible linkers, and even as intrinsically disordered. Several techniques exist to study protein structures, but small angle X-ray scattering (SAXS) has proven to be particularly powerful for the...

The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crysta...

The most important quantitative aspects of computational structural crystallography can be introduced in a satisfactory way using 1D truncated and periodic Gaussian functions to represent the atoms in a crystal lattice. This paper describes in detail and demonstrates 1D structural crystallography starting with the definition of such truncated Gauss...

KAMO and Blend provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending Blend to support additional clustering options to increase the sensitivity to differences in unit cell parameters and to...

X-ray diffraction from crystals of membrane proteins very often yields incomplete datasets due to, among other things, severe radiation damage. Multiple crystals are thus required to form complete datasets, provided the crystals themselves are isomorphous. Selection and combination of data from multiple crystals is a difficult and tedious task that...

Protein microcrystallography, which analyzes crystals smaller than a few tens of microns, is becoming one of the most attractive fields in structural biology. To realize the complete potential of this technique, it is inevitable that microcrystallography has to be combined with novel data collection instruments and strategies. Recently, a highly br...

Slides from the SBGrid webinar hosted on 9th February 2016. The link for the webinar is: https://www.youtube.com/watch?v=icEaCTiqW60

The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates ( in situ ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication o...

Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-genera...

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers t...

Crash course on the R software for users of CCP4 programs.

Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side...

This short article questions and investigates the possible range of values for the three angles of a unit cell in the triclinic system. Although no constraints are reported in manuals and tables for crystallography, the three angles are not really independent; the range of allowed values is calculated and presented in this paper.

The reciprocal lattice is derived through the Fourier transform of a generic crystal lattice, as done previously in the literature. A few key derivations are this time handled in detail, and the connection with x-ray diffraction is clearly pointed out. The Ewald sphere is subsequently thoroughly explained and a few comments on its representation in...

The two-dimensional Fourier transform (2D-FT) is well suited to the extraction of features to differentiate image texture, and the classification of images based on information acquired from the frequency domain provides a complementary method to approaches based within the spatial domain. The intensity, I, of the Fourier-transformed images can be...

In the context of discrete Fourier transforms the idea of aliasing as due to approximation errors in the integral defining Fourier coefficients is introduced and explained. This has the positive pedagogical effect of getting to the heart of sampling and the discrete Fourier transform without having to delve into effective, but otherwise long and st...

Lesson for the module Mathematical Physics II, Dept of Physics, University of York - Years 2005 - 2007

Lesson for the module Mathematical Physics II, Dept of Physics, University of York - Years 2005 - 2007

Lesson for the module Mathematical Physics II, Dept of Physics, University of York - Years 2005 - 2007

Lesson for the module Mathematical Physics II, Dept of Physics, University of York - Years 2005 - 2007

Lesson for the module Mathematical Physics II, Dept of Physics, University of York - Years 2005 - 2007

Lesson for the module Mathematical Physics II, Dept of Physics, University of York - Years 2005 - 2007

ACORN has been shown to be a successful program for the solution of small and medium-size protein structures, when data at atomic resolution or better are available. At the heart of ACORN lies a density modification method called DDM (Dynamic Density Modification). DDM operates on any density map containing a minimum of information. Its action is t...

An ab initio method is described for solving protein structures for which atomic resolution (better than 1.2 A) data are available. The problem is divided into two stages. Firstly, a substructure composed of a small percentage ( approximately 5%) of the scattering matter of the unit cell is positioned. This is used to generate a starting set of pha...

The positivity of the Patterson function is used as prior information for the decomposition of a powder diffraction pattern. An automatic procedure is described which, integrated with the Le Bail method, is able to provide estimates of |F| values that are often remarkably better than those obtained by application of standard techniques. The procedu...

Pseudotranslational symmetry may be characterized by the performance of statistical calculations on the normalized structure factors. The efficiency of the method is quite high if single-crystal data are used. When only powder data are available, the characterization process is not straightforward; in this paper, it is shown how it can safely be do...