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To configure the external crystal, go to the .cydwr file; select the Clocks tab at the bottom and double click on the system clocks. The clocking tree dialog box will appear allowing you to enable and describe the Xtal crystal. Also, please note there are known issues with the External MHz crystal and ES2-versions of silicon. Please reference the CY8C38 errata for details here: http://www.cypress.com/?docID=21289