Balls and sticks

Fig. 7. Snapshots of rupture taken (A) at the start of the simulation (zcant = 0), (li) at ZcB.nl = 2.8 A, (C) at Zcnm = 4.1 A, (D) at Zcnm = 7.1 A, and (E) at Zcant = 10.5 A. The biotin molecule is drawn as a ball-and-stick model within the binding )ocket (lines). The bold dashed lines show hydrogen bonds, the dotted lines show selected water bridges.

Figure 2-123. The most coinmon molecular graphics representations of phenylalanine a) wire frame b) capped sticks c) balls and sticks d) space-filling.

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

Figure 2-124. The most common molecular graphic representations of biological molecules (lysozyme) a) balls and sticks b) backbone c) cartoon (including the cylinder, ribbon, and tube model) and of inorganic molecules (YBajCujO , d) polyhedral (left) and the same molecule with balls and sticks (right),...

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. 

When we graph the positions of all six atoms in the x, y plane, the approximate nature of the input file is evident. Anyone who has used simple ball and stick molecular models will see that the carbon atoms in Fig. 4-4 are too close together and the entire molecule is compressed in the -direction. 

Molecules can be rendered as stick figures, ball and stick, CPK, and ribbons. Dot surfaces can also be included. Some regions were incorrectly shaded for small molecules on our test system running at 800 x 600 resolution with 24-bit color. The display uses a black background, but graphics are saved or printed with a white background. Overall, the rendering is adequate. 

Molden can display molecular geometries in a variety of formats, including lines, tubes, ball and stick, ribbons, and CPK. The user has some control over colors and sizes. Molden also has features designed for the display of proteins and crystal structures. The display can be exported as postscript, VRML, Povray, and image files. It can also be configured as a chemical mime viewer. 

WebLab Viewer gives a very-high-quality display suitable for publication and presentation. Molecules can be displayed as lines, sticks, ball and stick, CPK, and polyhedrons. In addition, different atoms within the same structure may be displayed in different ways. Text can be added to the display as well as labeling parts of the structure in a variety of ways. The user has control over colors, radii, and display quality. The program can also replicate a unit cell to display a crystal structure. Several types of molecular surfaces can be displayed. 

The earliest ball and stick models were exactly that wooden balls in which holes were drilled to ac commodate dowels that connected the atoms Plastic versions including relatively inexpensive student sets became available in the 1960s and proved to be a valuable learning aid Precisely scaled stainless steel framework and plastic space filling models although relatively expensive were standard equipment in most research laboratories... 

FIGURE 1 6 Molecular models of methane (CH4) (a) Framework (tube) models show the bonds connecting the atoms but not the atoms themselves (b) Ball and stick (ball and spoke) models show the atoms as balls and the bonds as rods (c) Space filling models portray overall molecular size the radius of each sphere approximates the van der Waals radius of the atom (d) An electrostatic potential map of methane... 

Ball and stick model (Section 1 10) Type of molecular model in which balls representing atoms are connected by sticks representing bonds Similar to ball and spoke models of Learning By Modeling... 

Acyclic Compounds. Different conformations of acyclic compounds are best viewed by construction of ball-and-stick molecules or by use of Newman projections (see Fig. 1.2). Both types of representations are shown for ethane. Atoms or groups that are attached at opposite ends of a single bond should be viewed along the bond axis. If two atoms or groups attached at opposite ends of the bond appear one directly behind the other, these atoms or groups are described as eclipsed. That portion of the molecule is described as being in the eclipsed conformation. If not eclipsed, the atoms... 

Panel 1.1 The 20 different amino acids that occur in proteins. Only side chains are shown, except for the first amino acid, alanine, where all atoms are shown. The bond from the side chain to Ca is red. A ball-and stick model, the chemical formula, the full name, and the three-letter and one-letter codes are given for each amino acid. 

All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves. These are difficult to illustrate. Therefore we use different types of simplified representations, including space-filling models ball-and-stick models, where atoms are spheres and bonds are sticks and models that illustrate surface properties. The most detailed representation is the ball-and-stick model. However, a model of a protein structure where all atoms are displayed is confusing because of the sheer amount of information present (Figure 2.9a). 

Figure S.22 Chemical formula for sialic acid (a-5-n-acetylneuramlnlc acid) drawn In approximately the same orientation as the ball and stick models in Figure 5.24. Ri and Rz which are H atoms in sialic acid, denote substituents introduced to design tightly bound inhibitors. These are large and hydrophobic as shown in Figure 5.24.

Figure 14.1 Each polypeptide chain in the collagen molecule folds into an extended polyproline type II helix with a rise per turn along the helix of 9.6 A comprising 3.3 residues. In the collagen molecule three such chains are supercoiled about a common axis to form a 3000-A-long rod-like molecule. The amino acid sequence contains repeats of -Gly-X-Y- where X is often proline and Y is often hydroxyproline. (a) Ball and stick model of two turns of one polypeptide chain.

Figure 15.16 Detailed views of the environment of Gin 121 in the lysozyme-antilysozyme complex. Gin 121 in lysozyme is colored green both in the space-filling representation to the left and in the ball and stick model to the right. This side chain of the antigen fits into a hole between CDR3 regions of both the heavy (Tyr 101) and the light (Trp 92) chains as well as CDRl from the light chain (Tyr 32). (After A.G. Amit et al.. Science 233 747-753, 1986.)...

Fig. 9. Ball-and-stick model for a 19.2° fullerene cone. The back part of the cone is identical to the front part displayed in the figure, due to the mirror symmetry. The network is in armchair and zigzag configurations, at the upper and lower sides, respectively. The apex of the cone is a fullerene-type cap containing five pentagons.

Let s return to bromochlorofluoromethane as a simple example of a chiral molecule. The two enantiomers of BrCIFCH are shown as ball-and-stick models, as wedge-and-dash drawings, and as Fischer projections in Figure 7.6. Fischer projections are always generated the same way the molecule is oriented so that the vertical bonds at the chirality center are directed away from you and the horizontal bonds point toward you. A projection of the bonds onto the page is a cross. The chirality center lies at the center of the cross but is not explicitly shown. 

Also shown are the one-letter and three-letter codes used to denote amino acids. For each amino acid, the ball-and-stick (left) and space-filling (right) models show only the side chain. (Irving GSs)... 

Figure Three represernarions of the structure of Cm- (a) normal ball-and-stick model (b) the polyhedron derived by truncating the 12 vertices of an icosahedron to form 12 symmetrically separated pentagonal faces (c) a conventional bonding model.

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