Using the model-profile.py script I can produce a .profile file which
can be read by the dopeplot perl script to generate 2 .dat files and a
.png image of the DOPE scores. Firstly, the .png that i get just plots
the psudoenergy of the template against that of the target, instead of
plotting both energies against residue number (attached). Has anyone
else encountered this problem?
When I try and just strip the energies from the final line of the
.profile (s) and plot them using GNUPLOT, I can get a plot, but the
problem (I think) is that my target and template are of different
lengths, so I am unsure how to interpret the differences in the energies
as i dont think the gaps in alignment are taken into account? I
suppose I could add these gaps manually but I would hope there would be
a better way of doing this? the dat files of the target and template
are attached.
I can't comment on the dopeplot perl script, since that's
user-contributed, but DOPE scores are not normalized, so you can't
compare DOPE profiles for model and template in any systematic way - at
best you can compare them by eye.