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