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Re: [modeller_usage] modeling an oligomer

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?


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:


and here:


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?