[modeller_usage] modeling an oligomer

[Douglas Kojetin <douglas.kojetin@gmail.com>]

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