Last modified on 23 February 2012.


The RNA2DMap application requires a Flash version of 9.0.115 or greater.


The VARNA application for displaying RNA secondary structures requires JAVA to be installed on your local machine.

If you are using FireFox and the display box shows only black, we suggest that you try accessing the page with either Chrome or Internet Explorer.

Another option is to use the VARNA applet available for download at:


Windows, Linux, UNIX

In addition to installing the normal RasMol package (which you can obtain from, you will need a script to intepret our RasMol files. Windows users should download this script, and install it somewhere on their system. UNIX/Linux users should use this instead. After editing the scripts to ensure that they contain the right path to the RasMol binary, you need to set the script up as the handler for the application/x-rasmol MIME type. This is done:

  • Internet Explorer
  • Currently IE doesn't appear to work with our script. Please use Firefox.
  • Firefox:
  • For firefox, first try to download the test script below. If you do not have an application set up, it will prompt you to select one. Simply browse to the location where you have stored our RASMOL script

    If firefox has already been told to use the RASMOL program, then you'll need to update it to use the script:

    • Open the Options windows (Tools->Options) or Preferences on UNIX (Edit->Preferences).
    • Select the Download tab or on UNIX the Content tab.
    • On Windows click the "View ¬† Edit Actions..." button in the Download Actions section of the Download tab. On UNIX click the "Manage..." button in the File Types section of the Content tab.
    • In the list box, find the RASMOL extension, and highlight it. Click the "Change Action..." button. Click the "Browse..." button and navigate to the place where you saved out script. Once the script is selected as the helper application, then close out of the Preferences/Options windows.

    These instructions may need to be tweaked depending on the level of your firefox.

Mac OS X

We are currently investigating the use of RasMol on both PPC and Intel Macintosh systems running MacOSX.

Test Your Setup

To test your ability to see our RasMol scripts download this sample script. Then compare it to these two images:

RasMol OK: RasMol NOT OK:

Data Windows:

For some large data sets or help files, we have chosen to spawn new windows (or tabs) for their display. Should you wish to keep more information on screen, please use your browser's features to open links in new windows/tabs.

All links to external web sites should appear in separate tabs/windows.

Graphics Files and Image Formats:

From each section of this site, you may access a series of graphics which will help you to fully understand the presented analysis.

Data Compression Formats:

Several different formats for data compression are in use at the CRW Site. Here, we list these formats and provide information regarding decompression programs.


A free replacement for the Unix compress utility, from the GNU Project. Source code and executables for multiple platforms are available from History may be found at Wikipedia.


Unix "tape archive" format (see Wikipedia for history). GNU tar is available for multiple platforms from GNU tar.


A common archival file format with a long history (see Wikipedia for details).

  • Windows: Native support in Windows XP and above.
  • Mac OS: Native support in 10.3 and later.
  • *nix (and others): Info-ZIP.

Stuffit Expander:

This free utility offers expansion of multiple file formats for Windows and Macintosh users. (

Software and Technologies Used:

We have used a range of software and technologies to prepare the CRW Site. We provide links to these items in the hope that you find these tools useful.

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MySQL database server mySQL
Microsoft SQL Server database server SQL Server
Adobe Reader Adobe Reader
PHP Hypertext Preprocessor PHP
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