Hello,

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.

class MyPeptide(loopmodel):
    def select_loop_atoms(self):
        # 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

m.make()

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

Greetings

Ignacio