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Re: [modeller_usage] question regarding homology modeling of an oligomer

On 7/30/15 9:39 PM, Monoj Mon Kalita wrote:

I have an NMR structure of an oligomer which belongs to transmembrane
domain region. Also, I have the single extramembrane region (X-ray
crystal) of that TMDs. Now my question is how can I dock that
extramembrane part on that oligomer and ask the program to replicate it
to the same symmetry of the oligomer ! Can modeller do like that ?

This sounds like http://salilab.org/modeller/FAQ.html#1
Modeller can reproduce the structures of the individual proteins just fine, but if you don't have interaction data it won't dock them automatically - it is not a docking program. If you dock your two input structures together and give them to Modeller as a single template with two chains, it should do what you want. 
	Ben Webb, Modeller Caretaker
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