[modeller_usage] structural alignment of models respect template(s)

Hi,

I am interested in making a 3D structural alignment of the resulting models with their template(s). I have included the "a.final_malign3d = True" line in the script as stated in the manual, and the *_fit.pdb files were generated. However, none of the models are correctly aligned to the template.

I wonder if anyone knows a successful way to align the models with just one modeling script. I could provide inputs and outputs if necessary.

Thanks in advance.

Best regards,