Re: [modeller_usage] [Peptide Refinement] How to move R groups only?

[Modeller Caretaker <>]

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
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