Wire Frame Model

Edge-oriented models (wire frames) Surface-oriented models Volume-oriented models... 

As a point of interest, it is possible to form very thin films or membranes in water, that is, to have the water-film-water system. Thus a solution of lipid can be stretched on an underwater wire frame and, on thinning, the film goes through a succession of interference colors and may end up as a black film of 60-90 A thickness [109]. The situation is reminiscent of soap films in air (see Section XIV-9) it also represents a potentially important modeling of biological membranes. A theoretical model has been discussed by Good [110]. 

The most well-known and at the same time the earliest computer model for a molecular structure representation is a wire frame model (Figure 2-123a). This model is also known under other names such as line model or Drciding model [199]. It shows the individual bonds and the angles formed between these bonds. The bonds of a molecule are represented by colored vector lines and the color is derived from the atom type definition. This simple method does not display atoms, but atom positions can be derived from the end and branching points of the wire frame model. In addition, the bond orders between two atoms can be expressed by the number of lines. 

The capped sticks model can be seen as a variation of the wire frame model, where the structure is represented by thicker cylindrical bonds (figure 2-123b). The atoms are shi unk to the diameter of the cylinder and ai e used only for smoothing or closing the ends of the tubes. With its thicker bonds, the capped sticks model conveys an improved 3D impression of a molecule when compared with the wire frame model. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

To extend these calculations to cylinders is more complicated, as both the position and orientation of a cylinder must be obtained. To do that we followed the sequence of operations used to position each cylinder, as shown in Fig. 32a, for particle 1, the lower front particle in the wall segment (note that wire frames of the previous positions are retained in each sketch for comparison). Similar sequences were available for each of the other particles in the wall segment model. 

Figure 2.8 Part of a polyethylene oxide chain using wire frame and space-filling models.

You go to the blackboard and begin to sketch. There s another way to draw a hypercube. Notice that if you look at a wire-frame model of a cube with its face directly in front of you, you will see a square within a... 

Figure 4.5 A wire-frame model of a cube viewed head-on and a tesseract.

Fig. 3. Examples of 5-HT3 agonist and antagonist pharmacophores. Serotonin (A) and granisetron (B) are shown as examples of 5-HT3 receptor agonists and antagonists. Both molecules are shown as stick models. Electrostatic potential is displayed in wire frame. Attention has been drawn to the important features of each pharmacophore.

We often use multiple styles of graphical representation to see different aspects of molecular structure. Typical images of a protein structure are shown in Figure 5.5 (see also color plate). Flere, the enzyme barnase IBNl (Buckle et al., 1993) appears both in wire-frame and space-filling model formats, as produced by RasMol (Sayle and Milner-White, 1995). 

The wire-frame image in Figure 5.5a clearly shows the chemistry of the barnase structure, and we can easily trace of the sequence of barnase on the image of its biopolymer in an interactive computer display. The space-filling model in Figure... 

The fourth area in which we have introduced students to computational chemistry at the first year level is in the field of molecular model building and molecular mechanics. We provide exercises in which the student is required to build and optimize the molecular structure of water and of dimethyl ether using the MM2 force field. Students compare the bond angles around the O atom in the two cases and examine wire frame, ball and stick, and CPK models of the molecules. They also explore the stereoisomers of carvone. One of these stereoisomers has dill scent and the other spearmint. Samples of the two isomers are available in the laboratory where the students do the molecular modeling. 

The structures shown in Eigure 15.17 illustrate the result of computer modeling of foams. A thin membrane connects the structural ribs, as in a soap bubble in a wire frame. Since this film is amorphous, its surface energy is uniform and the film will be flat. The structure, of course. 

Lines and curves are considered as initial elements in shape model construction. Higher level entities, such as wire frames, surfaces, solid primitives, and form features, are defined in the context of simple or compound lines and curves. 

Wire frames with unified topology and geometry use the same entities as solid models but without face and surface definitions. Note that these wire frames are not the same representations as the wire frames in the early era of geometric modeling. When a wireframe model defines a shape unambiguously, a surface or solid model can be replaced by the simple wire frame for economical modeling. If necessary, a verified wire frame can be completed into a surface or solid. 

No fluid can enter or exit through the wire frame at the top, and the film surface is pinned there. At the bottom, the film drains into the bath (or pool) in the cuvette, from which the film is drawn. The bath is otherwise inert, and it is assumed that the film shape tends to a static meniscus shape over the bath. This assumption will allow boundary conditions over the bath to be specified. The details of the mathematical specification of the problem appear elsewhere [57-60] in this section, the focus is on simplified models and comparing results from them with the experimental results discussed previously. 

The Pherobase database is an extensive compilation of behavior-modifying compounds listed in the various pheromone categories aggregation, alarm, releaser, primer, territorial, trail, sex pheromones, and others. The database contains over 30,000 entries. Jmol images of molecules are shown. The molecules can be projected as either space-filling or wire-frame models. They can be rotated in 3-dimensional space. In addition, the database includes mass spectral, NMR, and synthesis data for more than 2,500 compounds. This is a fun site ... 

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