I am working on trying to build models of a protein that is shorter than the template. The gap between the model and the template is spatially big (~30 angstroms) and I could not configure modeller properly to deal with this. Up to now, modeller built models just deleting the part that I wanted, but it was unable to join the CAs of the remained boundaries of the deleted region. The models done by modeller always have two parts separated spatially: the before and the after the deletion. Does anybody have a guess how to solve this problem?