Part of   Helix

SStructView Quick Start

This page gives the basic steps for integrating SStructView 1.1 into your web page.

1. Download the applet
   Download the SStructView.zip archive and place it in the same directory as your web page. You do not need to unzip this file. In fact, it is much faster for browsers to download the entire zip archive and then uncompress it internally to the browser to get at the Java classes.

2. Download the data file
   SStructView displays graphics defined in a data file that contains the 2D coordinates of bases in the secondary-structure diagram. Because of Java applet restrictions, this file must reside on the same server as your web page. Since you cannot use the data files directly from our server, you must copy them to your server first. Do this now by viewing e.coli16s.coord and choosing "Save..." from your Browser's File menu to save the file into the same directory as your HTML page.

   Note that the data file format has changed slightly since release 1.0; see

3. Place the applet inside an HTML page
   The <APPLET> and </APPLET> tags tell your browser to insert an applet into your web page. To insert SStructView into your web page, copy the following HTML snippet and paste it into your HTML file:

   
   <APPLET CODE="SStructView.class" ARCHIVE="SStructView.zip" NAME="SSApplet" WIDTH="500" HEIGHT="300" ALIGN="BOTTOM">
   <PARAM NAME="action-URL" VALUE="http://www-smi.stanford.edu/cgi-bin/generic.pl?selection=<--SELECTION-->">
   <PARAM NAME="structure-data-URL" VALUE="http://www-smi.stanford.edu/projects/helix/sstructview/data/e.coli16s.coord">
   <PARAM NAME="action-desc" VALUE="Generic CGI">
   <PARAM NAME="initial-selection" VALUE="7,8,9,10,11,12">
   <PARAM NAME="flagged-bases" VALUE="2,3,4">
   <PARAM NAME="show-controls" VALUE="true">
   </APPLET>
   

4. Tell the applet where to find the data file
   The "structure-data-URL" parameter in the HTML snippet above tells SStructView where to find the data file. Change the VALUE of the "structure-data-URL" parameter in the HTML snippet you just pasted to the URL for the data file you just downloaded and saved. For example, if your directory looks like this:
   

   then your "structure-data-URL" parameter would look like this:

   <PARAM NAME="structure-data-URL" VALUE="http://www.mysite.com/myHTMLdir/e.coli16s.coord">

5. Save your work and try it out!
   Save your web page to disk, and upload the whole directory to your web server (if necessary). Then load the page with your browser to try the applet!

   For an example of a more sophisticated web page that uses all of SStructView's features, see the SStructView tutorial page.

Details

• You can place the SStructView.zip file anywhere on your web site; just make sure the ARCHIVE tag points to the correct location. For example,
  

  ARCHIVE="http://www.mysite.com/javastuff/SStructView.zip"

• Structure-data-URL points to a data file; it must be on the same server as the Applet. Action-URL points to a CGI; it can be on any web server.

• Flagged bases are always drawn with black circles. Bases in the initial-selection remain selected until the user clicks on another base.

• The file format for SStructView 1.1 is slightly different than for SStructView 1.0; you will need to update your old files. See Secondary Structure Data File format for details.