On 8/25/18 9:52 AM, Ahmad Khalifa wrote: > Can I get an alignment in fasta format between two proteins using > modeller? Can I convert the pir or par format to fasta? Sure, alignment.write() can write out in FASTA format. See https://salilab.org/modeller/9.20/manual/node293.html for an example. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage