Structural information, visualizing

During the study of inorganic chemistry, the structures for a large number of molecules and ions will be encountered. Try to visualize the structures and think of them in terms of their symmetry. In that way, when you see that Pt2+ is found in the complex PtCl42 in an environment described as D4h, you will know immediately what the structure of the complex is. This "shorthand" nomenclature is used to convey precise structural information in an efficient manner. Table 5.1 shows many common structural types for molecules along with the symmetry elements and point groups of those structures. 

There are three potential methods by which a protein s three-dimensional structure can be visualized X-ray diffraction, NMR and electron microscopy. The latter method reveals structural information at low resolution, giving little or no atomic detail. It is used mainly to obtain the gross three-dimensional shape of very large (multi-polypeptide) proteins, or of protein aggregates such as the outer viral caspid. X-ray diffraction and NMR are the techniques most widely used to obtain high-resolution protein structural information, and details of both the principles and practice of these techniques may be sourced from selected references provided at the end of this chapter. The experimentally determined three-dimensional structures of some polypeptides are presented in Figure 2.8. 

Dark field Visualization technique for ashes produced by microincineration and fluorescence microscopy useful for low-contrast subjects Electron systems imaging EM shadowing Detection, localization, and quantitation of light elements Structural information from ordered arrays of macromolecules... 

DIAMOND — Visual Crystal Structure Information System (2001) CRYSTAL IMPACT, Postfach 1251, D-53002 Bonn, Germany. 

Most structural information is gained from the less intense (e 2000-20 000) satellite peaks which appear, for metal-free, neutral porphyrins, between 500 and 700 nm. Visual inspection of the intensity ratios of these minor peaks enables four types of peripheral or methine substituent patterns to be identified, and these are shown in Figure 2. The etio ... 

A. Halm, L. Offen, D.W. Fellner. Visualization of complex molecular ribbon structures at interactive rates. In 8th International Conference on Information Visualization (IV), IEEE Computer Society Press, Los Alamitos, CA, 2004, pp. 737— 744. 

Techniques employing the ultraviolet (UV), visible, and near-infrared parts of the spectrum have the advantage of high sensitivity (single photon), high time resolution (femtoseconds), and moderate spatial resolution (on the order of 100 nm). Structural information is obtainable by infrared to radio-frequency techniques (e.g., magnetic resonance). Together, these techniques have enabled the visualization of individual molecules and the measurement of excited state dynamics from such molecules on the picosecond time scale. It is also possible to follow the time course of chemical reactions on the femtosecond time scale when... 

Pennington, W. T. DIAMOND Visual Crystal Structure Information System. J. Appl Cryst, 1999, 32, 1029. 

Consequently, there are approaches to convert NMR-derived order parameters into structural information in the form of conformational ensembles of proteins.10 11 Such ensembles, in contrast to those obtained by "conventional" NMR calculations, reflect directly the experimentally observed dynamics at the time scale probed by the parameter actually used. The latter set of structures, often denoted "dynamic conformational ensembles", have the advantage of direct visualization of the conformations available for the protein and can be compared to other conformers of the same protein obtained under different conditions (most prominently binding partners) in a straightforward manner. Structural ensembles can of course be "back-transformed" to residue-specific numbers such as local RMSD values which can be used to generate the representations described above. 

Project Prospect is at the time of writing the first real application of semantic enhancement to primary research literature. By using open standards such as the InChl and the Open Biomedical Ontologies, the aim was to remove the ambiguity of searching (this remains to be well integrated with the search engines), but the information is now held in a structured form that can make this happen. In this first implementation, the information is used to add a layer of additional information (visualizations and definitions) and identify relationships between our own related HTML articles. 

Higher order structural information is emerging for a variety of FASs, and it is likely that future holds models of each of these enzymes at atomic or near-atomic resolution. Electron microscopy has been useful in defining the overall shapes of the yeast [33] and chicken [34] enzymes. The fact that these enzyme complexes maybe directly visualized is a striking demonstration of the massive size of these complexes. While the overall structural organization of the various components of the bacterial FAS has not yet been elucidated, atomic resolution structures of several bacterial FAS components have been determined [35-37] and others have been crystallized [38]. 

The graphics associated with SEC capture its ability to reveal qualitative structural information in a visual format. The applications discussed show how peak displacement of the triple-detector chromatograms reflects polymer polydispersity (dex-... 

The unit cell is the smallest region of a crystal lattice that contains all the structural information about the crystal. So, the crystal lattice is visualized as a stack of multiple identical unit cells. Each unit cell has characteristic lengths and angles. There are seven types of crystal structures, each defined by the properties of its unit cell hexagonal, cubic, tetragonal, trigonal, orthorhombic, monoclinic, and triclinic. 

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