Structure Viewers

In the past several years, the software used to examine and display structure information has been greatly improved in terms of the quality of visualization and, more importantly, in terms of being able to relate sequence information to structure information. 

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 

With the advent of many homemade visualization programs that can easily he downloaded from the Internet, the reader is strongly cautioned to only use mature, well-established visualization tools that have been thoroughly tested and have im-dergone critical peer review. 

As mentioned above, several viewers for examining PDB files are available (Sanchez-Ferrer et al., 1995). The most popular one is RasMol (Sayle and Mihier-White, 

RasMol contains many excellent output formats and can be used with the Mol-script program (Kraulis, 1991) to make wonderful PostScript ribbon diagrams for publication. To make optimal use of RasMol, however, one must master its command-line language, a familiar feature of many legacy three-dimensional structure programs. 

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Figure 2-137. Screenshot of the 3D structure viewer and download options for the 3D structure generated on the CORINA web interface.

Fig. 16.3. Screen shots of PGVL Hub. It has two ways to display molecules and their properties (Structural Viewer panel and Table viewer panel). It has been integrated with SpotFire for data visualization. It also has a decision maker capable of handling numerical and textual data as well as user selections by hand.

The importance of visual inspection Visual inspection of reactants and product molecules offers a library designer tremendous value in terms of what product molecules can or cannot be synthesized to help formulate and address SAR hypotheses. Project medicinal chemists have fondly called this popular approach cerebral processing. PGVL Hub has provided a capable environment to enable this approach (e.g., Structural Viewer panel with many molecules per page for fast browsing, sorting of displayed molecules by molecular properties, and multiple color markers to label molecules for further processing). 

ChemDraw plug-in This is claimed as being more than a mere structure viewer or a slow Java applet, rather it runs as fast and is as familiar as the regular ChemDraw application. Available without charge, it enables searching of web databases by structure or substructure, and viewing of ChemDraw documents that others have placed on the web. http //www.camsoft.com... 

The functionality required for an ELN to handle these structures is a specialized structure editor allowing creation and visualization of residues, definition of residues as real structures, and combined search for substructures in both the compound and the residue. Some additional features in the structure viewer help to mark and emphasize residues of the structure, allow overlapping residues, and label residues. A flag indicates whether the residues are displayed in the current context or not. If more than one residue is available, it is possible then to show or hide individual residues of a structure. The structure editor may be independent of a primary editor that is able to handle complete structures that is, structures are created with an external standard editor, whereas residue definitions are performed with an embedded tool. Since most databases are not designed for storing incomplete information, an ELN has to provide an internal format to store incomplete structures. In fact, it stores every complete part of a structure in a conventional database and keeps the additional information about the missing parts. 

The results of a structure or reaction query are displayed in a hit list, ideally within an ELN software. The user can then create a new section in the electronic scientific document using any structure from the hit list, including metadata delivered by the database. By transferring the structure, an additional unique identifier from the external database needs to be kept that is, the created section has a hyperlink to the external system that allows opening the default structure viewer directly from the section. 

TOPS Visualization and Structure Viewers Topology cartoons of secondary structure arrangements of proteins from DSSP input http //www.sander.embl-ebi.ac.uk/tops EBI, Cambridge, UK, D. Gilbert et al. [307]... 

Rasmol Easy to use molecular structure viewer http //www.bemstein-plus-sons.com R. Sayle [309]... 

Cn3d Molecular structure viewer and plugin http //www.ncbi.nlm.nih.gov/Stmcture/CN3D/ cn3d.shtml NCBI, Bryant et al. ... 

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. 

Because the protein structure record IBNl has three barnase molecules in the crystallographic unit, the PDB file has been hand-edited using a text editor to delete the superfluous chains. Editing data files is an accepted and widespread practice in three-dimensional molecular structure software, forcing the three-dimensional structure viewer to show what the user wants. In this case, the crystallographic data... 

Hogue, C. W. V (1997) Cn3D a new generation of three-dimensional molecular structure viewer. Trends Biochem. Sci. 22, 314—316. 

Chime Pro an enhanced structure viewer plug-in that extends the capabilities of Chime, allowing researchers to build ISIS structure and data queries and display search results as a table of structures directly in an HTML page. 

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