On Mon, Mar 15, 2004 at 04:10:58PM +0900, Han Choe wrote: > How do I denote pyroglutamate as one letter in the alignment file? I > tried small "p" but it did not work. In three letter, I use "PCA". That's correct, but there are no parameters defined for PCA, which is probably what's causing your problem. You will have to add suitable parameters yourself - see http://salilab.org/modeller/FAQ.html#17 Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage