Last modified on 23 February 2012.

• RNA2DMap
• VARNA
• RasMol
• Data Windows
• Graphics Files and Image Formats
• Data Compression Formats
• Software and Technologies Used

RNA2DMap:

VARNA:

Another option is to use the VARNA applet available for download at: http://varna.lri.fr/downloads.html

RasMol:

In addition to installing the normal RasMol package (which you can obtain from www.rasmol.org), 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:

Graphics Files and Image Formats:

• The RNA figures (secondary structures) at this site were generated with the graphics program XRNA developed by Bryn Weiser (University of California, Santa Cruz; formerly available from XRNA) for Sun Microsystems' Solaris operating system.
• GIF, JPEG, and PNG images are utilized as appropriate for the type of information shown in an image.
• Some images, our secondary structure diagrams in particular, are offered in PostScript format for printing. The Ghostscript package may be useful if you do not already have PostScript-compatible image tools installed on your system.
• To view PDF images in this site, you need the program Adobe Reader and a compatible browser.

Data Compression Formats:

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

tar:

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

zip:

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. (http://www.stuffit-expander.com/stuffit-expander.html).

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.

apache web server
MySQL database server
Microsoft SQL Server database server
Adobe Reader
PHP Hypertext Preprocessor
Ultimate Drop Down Menu 4