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