[modeller_usage] Refining part of a model using another structure as reference

Hi,

I have two questions/problems:

1. I need some help refining part of a model using another structure as reference. I tried the 'model-segment.py' script (https://salilab.org/modeller/manual/node23.html), but I'm unable to add the second structure (.pdb) to be used as the reference for the atoms that will be refined. 2. Is there a way to generate a model using only parts of two different structures? Like some residues from 'model1', and some from 'model2'. They are highly different sequences, so I tried modelling with multiple templates and got bad results.

Thanks in advance.