A diffraction pattern consists of a set of spots called reflections that result from capturing the image of an X-ray beam as it is scattered by the atoms in a crystal. Each reflection has a magnitude, which is experimentally accessible, and a phase, which is not. The inability to measure phase angles experimentally is known as the phase problem. Together, the magnitude and phase of a reflection constitute a quantity known as a structure factor. The set of structure factors provides the reciprocal-space representation of the structure, and the set of atomic coordinates provides the real-space representation. A Fourier transformation of the complex-valued structure factors leads directly to the real-valued electron density, which, after suitable interpretation, reveals the atomic positions and describes the molecular architecture of the crystalline material responsible for the scattering. Therefore, a solution to the phase problem requires an algorithm that will recover phase information that cannot be directly measured in the diffraction experiment.
Published in Chapter:
Molecular Structure Determination on the Grid
Russ Miller (Hauptman-Woodward Medical Research Institute and SUNY-Buffalo, USA) and Charles Weeks (Hauptman-Woodward Medical Research Institute, USA)
Copyright: © 2009
|Pages: 19
DOI: 10.4018/978-1-60566-374-6.ch017
Abstract
Grids represent an emerging technology that allows geographically- and organizationally-distributed resources (e.g., compute systems, data repositories, sensors, imaging systems, and so forth) to be linked in a fashion that is transparent to the user. The New York State Grid (NYS Grid) is an integrated computational and data grid that provides access to a wide variety of resources to users from around the world. NYS Grid can be accessed via a Web portal, where the users have access to their data sets and applications, but do not need to be made aware of the details of the data storage or computational devices that are specifically employed in solving their problems. Grid-enabled versions of the SnB and BnP programs, which implement the Shake-and-Bake method of molecular structure (SnB) and substructure (BnP) determination, respectively, have been deployed on NYS Grid. Further, through the Grid Portal, SnB has been run simultaneously on all computational resources on NYS Grid as well as on more than 1100 of the over 3000 processors available through the Open Science Grid.