albumns wrote: > how to evaluate which is the best model in "multiple template" > example? In the tutorial, it just use the model number 1 for the > final one. How to judge these models which is better than the left?

You can evaluate the model quality with the DOPE score (the model with the lowest DOPE score is most likely to be the best) in the same way as the single template example. It doesn't matter how many templates were used to build the model - the evaluation is of the model itself, not the alignment.

> my another question is that how can we draw the "basic model" and > multiple templates in the same diagram with GUNplot?

If you're referring to the plot of DOPE score profiles, shown at the end of the basic tutorial, such a plot is only qualitative at best. You can only plot a single profile in GNUPLOT, because with multiple profiles you have to account for the gaps. This is done by the plot_profiles script in the basic tutorial. To plot multiple templates, it should be straightforward to modify that script, adding extra calls to get_profile() and pylab.plot().

Ben Webb, Modeller Caretaker