Re: [modeller_usage] modeling an oligomer

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

As a followup, can I set my experimentally determined monomer  
structure (target) as six separate rigid bodies (chains A-F), then  
position the six rigid  target structures (chains A-F) separately to a  
chain of the template (chain A of the template to chain A of the  
target) based on a sequence alignment, then perform minimization?  Is  
this a good method and can someone explain how I might set this up?
Thanks,
Doug


On Aug 6, 2008, at 8:50 PM, Douglas Kojetin wrote:

> 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