I have a page with a navigation column and a data column that I wish to control separately, both sides use forms. When I scroll down and click on a button on navigation side I want the data side to change accordingly but I want the nav side to stay put (no repositioning).

My first two thoughts is frames or separate windows -- either is fine for me. But how can I control the data side from the nav side? Can I send a PHP script command to another frame/window or can PHP only affect the current window?

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Don't use frames! Use Ajax to refresh areas of the page without whole page refresh. It isn't as difficult as it seems. Both Prototype and jQuery libraries make updating a div with new data easy.

1) include the prototype library (<script>).
2) create a js file with your js functions.
3) create a php file which gets data.