model.seq_id — sequence identity between the model and templates

This is set by MODELLER during model building when model.transfer_xyz() is called. It is also read from or written to MODELLER-produced PDB files or mmCIF files (see model.write()).

You should set model.seq_id explicitly if you want to carry out GA341 assessment on a model not produced by MODELLER, as the sequence identity is not known in this case. See model.assess_ga341().