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; dlyumkis@scripps.edu; http://ami.scripps.edu
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