On 9/30/10 12:50 PM, dmitry lyumkis wrote: > I am currently using Modeller to predict a domain structure in a > protein of interest. The alignment that was calculated contains gaps > in the model, as compared to the template. When I finish modeling, I > would like to overlay the DOPE profiles between model and template, > but they contain a different number of residues, and therefore > graphical overlays do not make sense. I can get around this issue by > writing some script to get rid of extra residues or set their DOPE > energies to some constant value, but I was more interested in finding > out how this is normally done in Modeller? Is there some function that > would compare / align DOPE profiles for the calculated models based on > the template?

It never really makes much sense to compare the model with the template, since by construction the model will resemble the template. If you really want a comparison of DOPE profiles for the model and template, there is a script called plot_profiles.py as part of the basic tutorial on our website that will do it. This is only a qualitative (not quantitative) comparison though.

Ben Webb, Modeller Caretaker