Hi, For multiple templates try to follow this example: http://salilab.org/modeller/9.10/manual/node21.html Try to put those lines below, at the end of your script model-multiple.py script. It will display the top five models at the end of your model-multiple.log file. # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs)   # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) Regards, Flavio --- On Mon, 12/10/12, Krupal Jethava <krupal.jethava@gmail.com> wrote: From: Krupal Jethava <krupal.jethava@gmail.com> Subject: [modeller_usage] modeling with multiple sequence alignment. To: modeller_usage@salilab.org Date: Monday, December 10, 2012, 11:26 AM Dear Sir,   I am trying to use modeller for multiple sequence alignment but I got error while running script for DOPE score. will you guide from the beginning. how to make input file and which script should I use for that. Thanks.  -----Inline Attachment Follows----- _______________________________________________ modeller_usage mailing list modeller_usage@salilab.org https://salilab.org/mailman/listinfo/modeller_usage