Re: [modeller_usage] aligning DOPE profiles between model and template

[Modeller Caretaker <>]

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
--
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