[modeller_usage] Alignment missing

Dear Modeller team,

I need your quick suggestions and corrections on my scripts that I have been using to run on multiple computers. I am not getting any errors when I run the script3.py. But, when I compare the files .pap and .ali with other alignment servers like muscle, there are aminoacids missing in the alignment with Modeller. I don`t know where is the problem, if it is related to the alignmet with Modeller or if there is a problem in the script.py.

Best regards.

Paul Zair Leyva Miranda Laboratory of Molecular Modeling ESM-IPN