[modeller_usage] aligning DOPE profiles between model and template

[dmitry lyumkis <>]

Hi all,

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?

Dmitry Lyumkis
Automated Molecular Imaging Group, Department of Cell Biology
The Scripps Research Institute
10550 North Torrey Pines Road
c/o Dmitry Lyumkis, CB129
La Jolla, CA  92037
tel: (858) 784-9208; cell: (408) 772-1792; ; http://ami.scripps.edu