Image rendering

Figure 13.1 Correction of a structure by side-chain flipping. The original structure after CNS refinement is shown in (a) and after the recommended correction of WHATCHECK in (b). Carbon atoms are grey, oxygens white, and nitrogens black. Asn 144 and Glu 145 are the labelled adjacent residues in a helix, shown as a ribbon. After a 180 degree rotation about the chi-2 dihedral of Asn 144, the side chain amide nitrogen is now in position to hydrogen bond, shown as the labelled dashed line, to the carboxylate of Glu 145. Image rendered by ribbons.

A more sophisticated approach uses a stack of serial sections. Three-dimensional images in all forms of light microscopy are built up as serial sections. That is, the microscope (or other device) is focused at different depths through an object, and the resulting stack of images rendered as a three-dimensional object. This technique was introduced into Raman microscopy... 

Fig. 3. Molecular surface of hGH showing the different topographies of the Sitel and Site2 binding sites. In addition, the two sites possess quite different electrostatic properties (red negative charge, blue positive charge image rendered between 10 kT). (See Color Insert.)...

Figure 2 Cartoon representation of the Escherichia coli CPS heterodimer (1 JOB) showing residues (gray dotted spheres) that define the tunnels linking the three active sites in the enzyme. Subunits, domains, and ligands are colored as described in Figure 1. Image rendered In PYMOL.

Figure 3 Residues lining the ammonia tunnel of the Escherichia coii CPS heterodimer (1 JOB). The glutaminase site of the small unit is at the left and the carboxyphosphate-forming domain, containing bound ADP (CPK representation), is at the right. Side chains pointing into the tunnel are rendered as cylinders C - gray, O - red, and N - blue. Image rendered in PYMOL.

Figure 6 Superimposition of wiid-type CPS (red) (1 JOB) and the C248D CPS mutant (blue) (1T36) showing the structural changes when Cys248 is repiaced by an aspartate residue, image rendered in PYMOL.

Figure 8 Cartoon representation of the HisF/HisH heterodimer from Thermus thermophilus (1KA9). The HisF (cyciase) and the HisH (giutaminase) subunits are coiored biue and red, respectiveiy. image rendered in PYMOL.

Figure 9 Cartoon representation of the Saccharomyces cerevisiae IGPS/PRFAR complex in which Cys83 is covalently modified with acivicin (10X5) showing a cavity that is proposed to be part of the ammonia tunnel (gray dotted spheres). The giutaminase and cyclase domains are colored red and blue, respectively, and the acivicin and PRFAR moieties are rendered as CPK models C - gray, O - red, N - blue, and P - orange. Image rendered in PYMOL.

Figure 10 Close-up of the four layers of side chains located on /3-strands of the C-terminal (/3/a)g barrel, which define the interior surface of the ammonia tunnel in Saccharomyces cerevisiae IGP synthase (10X5). The PRFAR binding site is at the top of the tunnel, where the PRFAR ligand is shown asaCPK model C-gray, O-red, N - blue, and P-orange. Image rendered in PYMOL.

Figure 13 Cartoon representation of Salmonella typhimurlum IgPurL (1T3T). The N-terminal domain (1-140) is colored green, the linker domain (141-214) is colored yellow, the FGAM synthetase domain (215-979) is colored blue, and the glutaminase domain (980-1295) is colored red. Image rendered in PYMOL.

N -blue, P - orange, and S - yellow. Image rendered in PYMOL. 

Figure 34 Stereoview of the residues defining the ammonia tunnei in Fd-dependent Synechocystis GitS (1OFE) and crystaiiographic waters (red spheres). Residue side chains are shown as sticks. Coioring C - magenta (centrai domain residues) and green (FMN-binding domain residues), 0-red, N -biue, P-orange, and S-yeiiow. image rendered in PYMOL.

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