Re: [modeller_usage] read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file

On 01/13/2018 11:05 AM, Andrea Spinelli wrote: > I try to use python3, but it doesn't working. > > I can't understand why if I use my modeller module file in python > command prompt, it works. If I use the function in a script, not.

You have an elementary Python error in your script - not a Modeller problem. Your pir_export function never closes its file handle, so the alignment file is empty until the handle is flushed (at the end of the script, too late for Modeller). Simple solution would be to replace "pir_file.close" with "pir_file.close()". A better solution would be to use 'with' to open your file, as per https://jeffknupp.com/blog/2016/03/07/python-with-context-managers/

Ben Webb, Modeller Caretaker