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.