I want to model a chimera protein which consists of two individual
proteins. The crystallography of these proteins have not been reported,
I was only able to find the model for them. How can I build the chimera
based on models as templates?
See http://salilab.org/modeller/FAQ.html#1 for building a model of a
chimera. As long as you have PDB files for your "known" structures,
Modeller doesn't care whether these are real X-ray structures or models.