Hi, In the main method of the biojava-live Builder class the expression args[thisArg].substring(2) should be replaced with args[thisArg].substring(0). Regards, Les -- Dr. Lester Clowney AIST-NIBHT Structural Biology Centre 1-1 Higashi, Tsukuba shi, Ibaraki-ken 305-8566, Japan email: les@nibh.go.jp phone: +81-298-61-6540