(View thumbnails of all the figures)A series of illustrations demonstrate the capabilities of the program. The first six figures depict the types of drawings that can be made. Figure 1 gives the original line drawing style with the protein calmodulin (Babu et al., 1985). Figure 2 demonstrates the styles and textures available with the raster version. The protein ubiquitin (Vijay-Kumar et al., 1985) is colored according to amino acid type. Figure 3 shows how multiple ribbons may be superimposed using several previously aligned serine proteases. Figure 4 is a ribbon and base representation of a transfer RNA model. Figure 5 offers a view combining a double-stranded DNA representation along with a dimeric protein. The program will output ribbons in the format of the Wavefront visualizer bundled with the IRIS workstations. Figure 6 is a fanciful ray-traced rendering of the asymmetric unit of gamma-interferon. The four chains are given wooden textures and rest on a 50 A square marble base.
The next six figures deal with the types of analysis possible. Figure 7 shows the residues of ubiquitin color-coded by a mapping to the curvature/torsion values of the ribbon space curve. Note that this effectively highlights the classes of secondary structure and offers an alternative parameteriztion to the phi/psi values (compare to Figure 2 where the secondary structure is assigned by hydrogen bonding patterns). Figure 8 shows the residues of calmodulin color-coded by a mapping to phi/psi space. The Ramachandran plot displayed is based on an analysis of 40 highly refined proteins. Figure 9 gives a color mapping of the individual temperature factors in ubiquitin. Similar figures may be prepared to highlight residues whose chain dihedral values are not one of the allowed ``rotamers'' as determined by Ponder and Richards (1987). Figure 10 depicts the mainchain hydrogen bonding patterns in the N-terminal domain of calmodulin. This leads to an interesting means to visualize the helical dipoles. Figure 11 depicts the rms potential energy in the bonds, angles, and dihedrals of each residue in the vacinity of the active site of viral neuraminidase (Bossart et al., 1991). The program XPLOR (Brunger et al., 1987) was used to perform the analysis. Figure 12 shows the same region color coded by the real space R-factor of the side chains as calculated by the program O (Jones et al., 1991). In both figures, the hotter colors are meant to convey potential problems in the residue.