How to see 3D structures ?

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]

	[3D(image)]	[3D(Jmol)]	[3D(Chime-plugin)]	[3D(rasmol)]
Windows 95/98/NT/XP	O	O	O	X
Macintosh	O	O	O	X
Unix (Linux,SGI,Sun...)	O	O	X	O
[Necessary Softwares]	nothing	Java Runtime Environment(JRE)	Chime-plugin	RasMol

• View images [3D(image)]

  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.

• View using Jmol [3D(Jmol)]

  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.

• View using Chime-plugin [3D(Chime-plugin)]

  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:

  1. Access to the MDL homepage.
  2. System Requirements.
  3. How to Buy.
  4. If you are a new user, do "Register".
  5. Login
  6. Click "Download MDL chime..."
  7. START DOWNLOAD
  8. Double-click on the downloaded file to install.

  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.

• View using RasMol([3D(rasmol)])

  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:

  • Install RasMol on your own machine
    Get the source codes of RasMol from the site http://www.openrasmol.org/, compile and install it. For Linux users, pre-complied binaries are also available.

  • Configure you browser(Netscape version 4)
    1. Select [Edit]->[Preferences]->[Navigator]->[Applications]
    2. Click [New...]
    3. Input as follows, then click [OK].

          Description : RasMol Script
          MIMEType    : application/x-rasmol
          Suffixes    : [Don't input anything !!]
          Application : xterm -e rasmol -script %s
          

  After configuring, please click the link [3D(rasmol)] at the top of the page. If your browser is configured properly, the windows of xterm and rasmol appear to display a 3D structure. The operation is almost the same as that of normal RasMol. But two defined sets are prepared. The first one is "ALIGN", which is a set of aligned residues for the query sequence. The second one is "IDENTICAL", which is a set of the residues, that are identical to that of aligned query sequence. For example, if you want display the aligned region in yellow, and the identical regions in green, type in the command line of the xterm as follows:

  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