1. The latest version of Magento comes with a somewhat outdated version of the script.aculo.us effects file, which is part of the problem. Go get the latest version (1.8.2 right now). You may want to rename it with the version number at the end, like effects-1.8.1.js
2. Upload the file to [Magento]/js/scriptaculous
3. Open the file page.xml at [Magento]/app/design/frontend/default/default/layout/page.xml
4. On about line 41, there will be a line like this:

   <action method="addJs"><script>scriptaculous/effects.js</script></action>

   Change the file name to your new file

5. The layout files are normally cached, so you’ll need to clear that cache to see the effect take place. Log into the backend and go to System > Cache Management
6. Select “refresh” from the All Cache menu and save (which should clear your cache)
7. Reload a store page and view source to make sure your new file is the one that is loading
8. Now you need to include jQuery on your page. You could add a new line to the page.xml file, or you could open the common head.phtml file at [Magneto]/app/design/frontend/default/default/template/page/html/head.phtml – and add your <script> for jQuery there
9. The final step is making sure that jQuery is in .noConflict(); mode. This is the final step to making sure it plays nice with Prototype
10. Now you need to set noConflict and write code in that mode. Basically you replace the normal “$” with a new shorthand ($j, in this case).

    var $j = jQuery.noConflict();
    
    $j(document).ready(function(){
        $j("#test").css("padding","10px");
    });

Note, I didn’t invent this fix, I just wanted to consolidate information I found while researching this. Mostly came from the wiki and this thread, which you can reference for more information.

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