Charlie Allerston wrote: > 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.

Ben Webb, Modeller Caretaker