[modeller_usage] modeling an oligomer

Hi All,

I would like to create an oligomeric (hexamer) model. I have a Ca- only hexameric model (chains A-F) to use for the template and an experimentally determined monomer structure I would like to use for the target. Essentially, I would like to map six of the monomer target structures to chains A-F of the template. I've attempted to do this using the "model-myini.py" script as described here:

http://www.salilab.org/modeller/manual/node26.html

and here:

http://www.salilab.org/modeller/examples/automodel/model-myini.py

but my output hexamer structure ends up looking like spaghetti. Am I using the proper modeling script for this task? If so, what should the alignment and target PDB files look like to map the monomer structure to the hexamer structure?

Thanks, Doug