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Re: [modeller_usage] Using only partial information for the model

Stéphane Téletchéa wrote:
I'm willing to use modeller in a specific modelling procedure where only specific parts of the model are wanted. 
In fact, i have two beta sheets and two helices in the pdb template, and 
there are linked via loops.

I would like to know the procedure i need to follow in order to model 
only those subparts of the system (and use modloop for the linking part).

I'm not sure I quite follow what you want to do, but you can certainly 
build a model for only part of a sequence - just list only the sequence 
you want to model as the target in your alignment file. But for the 
loops you may as well model them anyway (you can always override 
select_atoms to instruct Modeller not to bother to optimize them) since 
ModLoop needs starting coordinates for the loop regions.

	Ben Webb, Modeller Caretaker
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