At the bottom of the result page of Pairwise 3D Alignment and Multiple 3D Alignment, you will find the following links.
3D VIEW:[3D(image)] [3D(Jmol)] [3D(Chime-plugin)] [3D(rasmol)] [superimposed PDB file]Among them, the first four links [3D(image)], [3D(Jmol)], [3D(Chime-plugin)], [3D(rasmol)] are for viewing a predicted 3D structure. Availabilities of these three links depend on your own computer and configuration:
|[Necessary Softwares]||nothing||Java Runtime Environment(JRE)||Chime-plugin||RasMol|
A click on [3Dstr(image)] leads to a display of the 3D structure by gif file, without the special plugins. Non-aligned regions are shown in blue, while aligned regions are painted in magenta (helices), yellow (sheets), or white (coils). In this display, you can neither modify the colors, nor rotate the figure.
The software Jmol is a WEB server applet written by JAVA language. If your browser has JRE(Java Runtime Environment), nothing more is necessary to use Jmol.
If you wish to change the viewing angle or the display mode, you need to install a special plug-in software to your computer. Please download the plug-in "Chime" from the MDL homepage. The Chime plug-in is a freeware, but you must register as a Chime user before you download the plug-in. As of July, 2001, the versions for Windows, Macintosh are available. To configure your browser, do the following:
In contrast to the view images, you can rotate the molecule by dragging a mouse on it. Furthermore, you can manipulate buttons at the bottom of the screen to display identical amino acids, ligands, or aligned regions only
Unfortunately, the versions of any UNIX machines are not developed. We recommend UNIX users to choose the next option "View using RasMol".
[CAUTION] We suggest Macintosh users to choose Netscape, as Explorer sometimes fails to work.
The UNIX machines can display 3D structures using the external application: xterm and RasMol. To configure your Netscape browser for RasMol operation, do the following:
Description : RasMol Script MIMEType : application/x-rasmol Suffixes : [Don't input anything !!] Application : xterm -e rasmol -script %s
RasMol> select ALIGN RasMol> color yellow RasMol> select IDENTICAL RasMol> color green
Please send your inquiries or comments on MATRAS to
LastModified:Feb 23, 2007