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Create .php page with below code to set “Is Anchor” to all categories in magento by custom php script.
error_reporting(E_ALL); ini_set('display_errors', '1'); // Load Up Magento Core define('MAGENTO', realpath('/')); require_once(MAGENTO . 'app/Mage.php'); $app = Mage::app(); $categories = Mage::getModel('catalog/category') ->getCollection() ->addAttributeToSelect('*') ->addAttributeToFilter('is_anchor', 0) ->addAttributeToFilter('entity_id', array("gt" => 1)) ->setOrder('entity_id'); foreach($categories as $category) { echo $category->getId() . "t" . $category->getName() . "n"; $category->setIsAnchor(1); $category->save(); }