I am working on predicting a structure of a protein from several templates. Each template has homologous sequences for different parts of the target protein. It seems however that only one template is picked up by Rosetta. Is there a tutorial or a manual for multiple template homology modeling with Rosetta? What is the format of input alignment file I should use? how should I specify paths to template pdb files in the flag file? Is there a way to specify which template should be used for specific sequences of the target protein (as there is an overlap in sequences of some template proteins and I would like to chose which template should be used for predicting specific part of the target protein).
Thank you for your insights.