Molecular graphic views

FIGURE 17.30 (a) A ribbon diagram and (b) a molecular graphic showing two slightly different views of the structure of troponin C. Note the long a-helical domain connecting the N-terminal and C-terminal lobes of the molecule. 

FIGURE 21.24 Molecular graphic images (a) side view and (b) top view of the Fj-ATP synthase showing the individnal component peptides. The 7-snbnnit is the pink strnctnre visible in the center of view (b). 

Figure 1. Molecular graphics (ANIMOL) views of the dihydro-xybenzenes. The gray atoms are carbons, the dark atoms are oxygens and the light atoms are hydrogens. a) ortho b) meta c) para.

Fio. 1. (a) A view of the influenza virus hemagglutinin trimer showing jV-acetylneuraminic acid (3, in CPK form) bound, (b) The tetrameric unit of influenza A virus sialidase. The figures were generated using the PyMOL Molecular Graphics System (Delano, W.L. (2002) at http // www.pymol.org). 

Wide range of graphic views and modeling techniques from molecular mechanics through rigorous electronic structure methods... 

Even though there may be an asymmetric centre in the backbone of a bisphosphine, if it prefers this Cs local symmetry for the phenyl groups, the enantiomeric character is not optimally passed onto the substrate coordinating to the Cs-diphos ligand-metal complex. Many crystal structures have been determined that support this view and refine it even further, as do molecular graphics (or molecular mechanics) for a broad range of ligands [55]. 

There are many other molecular graphics programs available two of the most popular are Chime (http //www.mdli.com/products/framework/chime/index.jsp) and RasMol [29] (http //www.umass.edu/microbio/rasmol/index2.htm) however, Cn3D and SRS 3D are our first choice for gaining an initial view of structures because of their ability to present sequence and structure in such an integrated way. 

Figure 9.1 Overall fold and disulfide pairing of BmorPBP. A) Secondary structure of BmorPBP. B) Side, top, and bottom views of BmorPBP with disulfide linkages and bombykol represented in stick form. C) Side, top, and bottom views of the BmorPBP asymmetric dimer. Images were prepared using PyMOL (Delano, W.L. The PyMOL Molecular Graphics System. (2004) DeLano Scientific, San Carlos, CA, USA. http //www.pymol.org).

Coming to the end, an attentive and informed reader may have observed that the solved problems that we have selected belong to a special group of research papers that have received limited acknowledgment, at least as reflected in their limited citations. This does not mean necessarily that a limited number of researchers have seen them and have been aware of some of them, which could be the case had they been published in some obscure scientihc journals. Because they have been published in outstanding journals, such as the Journal of the American Chemical Society, Tetrahedron, Journal of Physical Chemistry, Journal of Chemical Information and Computer Science, International Journal of Quantum Chemistry, Chemical Physics Letters, Journal of Computational Chemistry, New Journal of Chemistry, Journal of Mathematical Chemistry, SAP and QSAR in Environmental Research, Journal of Molecular Graphics and Modelling, and such, it is fair to assume that these papers may have been seen but, in view of their limited citations, tend to be avoided. 

In Chapter 7, Paul G. Mezey reviews molecular surfaces from a mathematical and chemical point of view. A molecule does not have a surface in the same sense that macroscopic objects do, yet the concept of a surface is important to molecular graphics and molecular modeling. Terry P. Lybrand in Chapter 8 provides an overview of molecular simulations based on empirical force fields. He shares his expertise as someone who has been an active contributor to this important approach to obtaining realistic representations of macromolecules. In view of the strides made in molecular dynamics and other simulation techniques in the last 10 years, as a result in large part to the availability of supercomputing, this review is especially apropos. 

Collapsing Can Liquid Nitrogen and Balloons Charles s Law A Graphical View Charles s Law A Molecular-Level View The Ideal Gas Law PV - nRT Visualizing Molecular Motion Single Molecule Visualizing Molecular Motion Many Molecules Kinetic-Molecular Theory/Heat Transfer Diffusion of Gases... 

Krieger, E., Vriend, G. YASARA View - molecular graphics for all devices - from smartphones to workstations. Bioinformatics 30(20), 2981-2982 (2014)... 

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