vidhya ganesh wrote: > I have questions on "Model evaluation" step in "Basic modeling". As > far as i know, if it is a best model,the dope score profile shows region > of low energy.But, the plot in my model with template looks as if some > residue position have relatively high energy and in some showing of low > energy.How can i judge whether it is a good model or bad?

The only qualitative score is the total score - not the profile. The most reliable method in Modeller is to calculate the normalized DOPE score, which is a z-score. Good models are likely to have z-scores of -1, -2 or better.

Ben Webb, Modeller Caretaker