[modeller_usage] Multidomain protein

Dear Sir, I am trying to model a protein which has three domains seperated by linker region in a linear fashion.Domain are not overlapping as they are seperated by linkers.By macromolecular docking I generated their best possible orientation and used as input PDB files.But the model given by modeller wont preserve the provided orientation and domain got seperated further by the linker regions.The template for linker region has streches of helixes seperated by coils. So what should I do to preserve the domain orientation and then generate the possible model or I should use any other approach? Waiting for your reply....

Research Student Ranjit Kumar