On 5/20/11 10:20 PM, Ignacio Ibarra wrote: > 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.
That isn't surprising, because you are selecting all atoms in residues 618:D through 630:D (which is presumably your short peptide):
> def select_loop_atoms(self): > # 13 residue selection > return selection(self.residue_range('618:D', '630:D'))
It's easy to select just the sidechain; use the only_sidechain() function: http://salilab.org/modeller/9.9/manual/node229.html
For example, the following should do what you want: def select_loop_atoms(self): return selection(self.residue_range('618:D', '630:D')).only_sidechain()
Ben Webb, Modeller Caretaker