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VIPERdb Visualization Tools

WebMol

Every virus info page displays a small, moveable rendering of the given virus using WebMol, a Java Applet created by Dirk Walther for the display of PDB files. A similar display is shown with the results of the Oligomer Generator. Double clicking on this small rendering will open the WebMol applet, which displays a larger representation of the PDB file. The applet provides a variety of different color coding schemes and viewing options, as well as a number of analytical tools such as distance matrices, ramachandran plots, and hydrogen bond detection. In order to view this applet your browser must have Java enabled. For more information about enabling Java, see the javascript page.

QuickPDB

QuickPDB is a Java Applet created by Ilya Shindyalov and Phil Bourne. QuickPDB will render the PDB file as an alpha-carbon trace of the backbone, which you can then color by selecting different coloring options on the left. You can additionally color sections by selecting them in the sequence, displayed above the structure. This Applet is only available for structures that have been submitted to PDB and have a valid PDB ID. You must have Java enabled in your browser in order for the applet to function. For information about enabling Java, see the javascript page.

The Cn3D Plugin

Cn3D is a plugin that can be downloaded from NCBI's Cn3D page. This versatile plugin will create a 3-dimensional display of the PDB file, which you can then choose to render in different styles (wireframe backbone, worm tube, etc.) as well as color to suit your needs. Cn3D can also display structure alignments of numerous proteins, which includes a number of display options for interpreting the alignments. Only structures that have been submitted to PDB and have a valid PDB ID can be viewed with this plugin.

The Chime2 Plugin

MDL Chemscape Chime is a plugin that can be downloaded and installed onto Windows, Mac, and SGI operating systems using the instructions found on out our Chime Plugin Page.


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