I'm using mod9.9 to model a short peptide-protein complex.
Once the model.pdb file is created, I would like to make a refinement
without moving the protein (it should be fixed), and readjusting the R
groups of the short peptide *with no movement of the backbone*. I don't
want to modify the positions of the backbone at all.
Currently I'm using the following code (short version). This one creates
a model with no movement of the protein, but the short peptide is
displaced several angstroms.
# 13 residue selection
return selection(self.residue_range('618:D', '630:D'))
m = MyPeptide(env,
inimodel='model.B99990001.pdb', # initial model of the target
sequence='refinedModel') # code of the target
m.loop.starting_model= 1 # index of the first loop model
m.loop.ending_model = 1 # index of the last loop model
m.loop.md_level = refine.slow
I think that I should add restraints like the "max_ca_ca_distance" one,
but I'm not sure if there's something more appropiate