nagaraju ngaraju wrote: > I want to do project in homology modelling using modeller but I am > unable to crete .pir file > Can you suggest me in this regard The alignment file is just a plain text file in a certain format. This format is described at http://salilab.org/modeller/9v5/manual/node440.html There are also plenty of examples of suitable alignment files in the Modeller distribution (examples directory) and the online tutorial. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage