WebMol viewer

WebMol JAVA PDB viewer to display and analyze structural information. 

Consider an example in which the sequence ELVISISALIVES is represented in the SEQRES entry of a hypothetical PDB file, but the coordinate information is missing all (x, y, z) locations for the subsequence ISA. Software that reads the implicit sequence will often report the PDB sequence incorrectly from the chemical graph as ELVISLIVES. A test structure to determine whether software looks only at the implicit sequence is 3TS1 (Brick et al., 1989) as shown in the Java three-dimensional structure viewer WebMol in Eigure 5.3. Here, both the implicit and explicit sequences in the PDB file to the last residue with coordinates are correctly displayed. 

Figure 5.3. Testing a three-dimensional viewer for sequence numbering artifacts with the structure 3TS1 (Brick et al., 1989). WebMol, a Java applet, correctly indicates both the explicit and implicit sequences of the structure. Note the off-by-two difference in the numbering in the two columns of numbers in the inset window on the lower right. The actual sequence embedded in the PDB file is 419 residues long, but the COOH-terminal portion of the protein is lacking coordinates it also has two missing residues. (See color plate.)...

Although the RCSB Weh site provides a Java-hased three-dimensional applet for visualizing PDB data, the applet does not currently support the display of nonprotein structures. For this and other reasons, the use of RasMol v2.7 is instead recommended for viewing structural data downloaded from RCSB more information on RasMol appears in the following section. If a Java-based viewer is preferred, WebMol is recommended, and an example of WebMol output is shown in Figme... 

Walther D. (1997) WebMol—a Java based PDB viewer. Trends Biochem. Sci. 22, 274-275. 

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