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