thanks for you help. should i use the the entire second template(loop is
disordered) sequence or only part of the disordered sequence to aglian?
You would definitely need to exclude the ligand and any part of the
sequence that interacts with the loop (otherwise Modeller will have a
hard time positioning the ligand, since it will get conflicting
information). But you can include the rest of the protein if you want -
since you said the sequences are very similar I doubt it would make much
difference either way.