> I finished modelling my protein and doing the evaluation step. I run the > file evaluate_model.py to calculate the DOPE score of my model. > I got DOPE score : -39521.605469 and there was no error in the log file. > > I use this profile file to generate the DOPE plot using GNUPLOT but this > program show a strange line. Actually It just show the position of my > aminoacid but no DOPE score for each.
That's because gnuplot by default will plot the first column on your y axis, and the first column in the profile file is just the residue number, so it'll plot [1,1], [2,2], [3,3] etc. - i.e. a line. You need to plot the last column (column 42) which is the total energy. In gnuplot you can do this with a command like
plot "myprotein.profile" using 1:42 with lines
Ben Webb, Modeller Caretaker