Query regarding visualizing profile in GNUPLOT
We run the evaluate_model.py which implements mdl.assess_dope function in modeller8v2. We got the DOPE score. Now we want to generate the PLOT using GNUPLOT with the output of the script. We tried in GNUPLOT, we just got a diagonal line but not like presented in the tutorial.
the script looks like:
from modeller import*
from modeller.automodel import*
log.verbose()
env=environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
#env.io.atom_files_directory='./:../atom_files'
mdl=model(env)
mdl.read(file='1fdx.B999900001.pdb')
aln=alignment(env)
code="1fdx_my"
aln.append_model(mdl,atom_files='1fdx.B999900001.pdb',align_codes=code)
aln.append_model(mdl,atom_files='1fdx.B999900001.pdb',align_codes=code+'-ini')
mdl.generate_topology(aln,sequence=code+'-ini')
mdl.transfer_xyz(aln)
mdl.assess_dope(output='ENERGY_PROFILE REPORT',file='1fdx_my.profile',
normalize_profile=True,smoothing_window=15)
Looking forward for reply
-P.Saravanan