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Re: [modeller_usage] (no subject)

doppelt olivia wrote:

I've been using MODELLER 2 ways :
first with only one template
second with 2 templates
Is the Objective Function of the modeles generated comparable ? and if so, how ? The first is around 600, and the second around 3000 for a 151 residus query sequence.
The objective function is the sum of all restraints, and so is only comparable if you have the same number and type of restraints, which is not the case here, so no, they are not comparable. You would be better advised to evaluate the models with an assessment method such as GA341 or DOPE (which will be comparable between models since your target sequence is the same). I would also advise you to build multiple models to ensure adequate sampling, not just a single one for each case. 

	Ben Webb, Modeller Caretaker
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             http://www.salilab.org/modeller/
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