On 4/26/19 11:00 AM, Bisignano, Paola wrote: > I would like to model missing portion of a solved protein structure by > using two different templates. I know that is pretty straightforward to > use multiple templates, but I would like to include restraints based on > the first entry only. Basically I would like to keep the first solved > structure as it is, and just move the residues lining the missing > portions, while using the second structure as a 'flexible' template.

Modeller generates restraints for all structures in the alignment. You will likely get better structures if you carefully create a good multiple alignment of both templates, and let Modeller use it. But if you really don't want to use information from one template as restraints, just leave it out of the alignment.

It is straightforward to only move part of the system, and to provide an initial model. See https://salilab.org/modeller/9.21/manual/node23.html https://salilab.org/modeller/9.21/manual/node27.html

Ben Webb, Modeller Caretaker