On 9/28/10 9:39 AM, Omar Piña wrote: > I am modelling a tetrameric protein (ion channel). I want to evaluate > the models, but I have read that the DOPE assesment is not good for > multi chain proteins > (http://www.salilab.org/modeller/9v6/manual/node242.html).

That's not correct - we simply have no benchmark data to prove whether it is good or bad. It has only been thoroughly tested on single chains. It *appears* to function rather well on multichain models, however.

> Then, how is > the best way to evaluate them? Each chain should be evaluated > independently? Should I take only the best molpdf score?

You certainly should not use the molpdf score - the Modeller scoring function does a great job for optimization, but it is not designed to discriminate good models from bad models at assessment time.

Ben Webb, Modeller Caretaker