Last modified on 28 July 2008.
- Printing
- The RNAMap Applet
- RasMol
- Data Windows
- Graphics Files and Image Formats
- Data Compression Formats
- Software and Technologies Used
Printing:
To facilitate easy printing of CRW Site information, we provide the "Print this Page" link, located in the header at the far right, which will display the page with a simpler header and appearance.
On pages where we have experienced printing problems (typically, on pages with complex tables), please use the "Download PDF" form to download a PDF of the page, which you may then print from your PDF viewer.
The RNAMap Applet:
The RNAMap applet requires version 1.5 of the JRE. Newer versions have caused problems in our internal testing.
Please note that your browser must allow pop-up windows for this site to have access to all of RNAMap's functionality.
The memory suggestions below will need to be tweaked depending on your OS and browser combination
For best results, this applet needs a larger-than-standard memory allocation (up to 500 MB for the 70S crystal structure applets). You can increase this allocation using the "Applet Control Panel," which is part of your JRE.
NOTE: this increase to the memory allocation must be done every time that your JRE is updated.
- MacOSX: Run the "Java Preferences" application from
Finder:Applications:Utilities:Java(the exact title of the application is version-dependent). Add "-Xmx500m" (without the quotes) to the "Java Runtime Parameters" box in the first tab of the application. - Windows and UNIX/Linux:
- First, open the Java Control Panel:
- Windows: Start -> Control Panels. Then, double-click the "Java" Control Panel.
- UNIX/Linux: run the program /usr/jdk/latest/bin/ControlPanel (the exact path may vary, depending on how you have installed your JRE).
- Select the Java tab, then click the View... button in the Java Applet Runtime Settings. Each JRE listed (there may be several) will have a box where you can set the runtime parameters. In that box, add the text "-Xmx500m" (without the quotes) and click "OK". Then, close the Control Panel.
- First, open the Java Control Panel:
RasMol:
Windows, Linux, UNIX
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
- 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.
If firefox has already been told to use the RASMOL program, then you'll need to update it to use the script:
These instructions may need to be tweaked depending on the level of your firefox. We use 1.5, but are upgrading to the 2.0 version.
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: |
|---|---|
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 |
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.
- 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:
Several different formats for data compression are in use at the CRW Site. Here, we list these formats and provide information regarding decompression programs.
gzip:
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 Vista.
- 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 |  |
