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1. Allow cream cheese, sour cream, and eggs to stand at room temperature for 30 minutes. Meanwhile, for crust, in a medium bowl combine crushed graham crackers, pecans, and 1 tablespoon sugar. Stir in melted butter. Press mixture onto the bottom and about 2 inches up the sides of an 8- or 9-inch springform pan; set aside.
2. Preheat oven to 375 degrees F. If using vanilla bean, use the tip of a small sharp knife to scrape out seeds; set aside. In a large mixing bowl beat cream cheese, sour cream, 1 cup sugar, and flour with an electric mixer on medium speed until combined. Add eggs; beat just until combined. Divide batter in half. Stir orange peel and food coloring into half of the batter. Stir vanilla seeds or vanilla bean paste (if using) into the remaining batter.
3. Pour orange batter into crust-lined pan, spreading evenly. Spoon vanilla batter over orange layer, gently spreading evenly. Place springform pan in a shallow baking pan. Bake for 45 to 55 minutes for the 8-inch pan, 40 to 50 minutes for the 9-inch pan, or until a 2 1/2-inch area around outside edge appears set when gently shaken.
4. Cool in pan on a wire rack for 15 minutes. Using a small sharp knife, loosen crust from sides of pan; cool for 30 minutes more. Remove sides of pan; cool cheesecake completely on wire rack.
5. Spoon marmalade over top of cheesecake; carefully spread to outside edge.* Cover and chill for at least 4 hours before serving. If desired, garnish with orange wedges. Store any leftover cheesecake, covered, in the refrigerator for up to 3 days.