Hi,

while you can exclude any atoms from refinement,

refinement {
refine {
    sites {
      individual = not (chain Z and resseq 1:123)
    }
}
}

that will refine coordinates of everything but atoms in "chain Z and resseq 1:123",

I guess you can handle this situation more elegantly. Can you please send me PDB file or its portion containing relevant residues (before and after refinement, so I see how they pushed apart), and I might be able to suggest a better solution.

Pavel

On 5/22/14, 9:13 PM, Murpholino Peligro wrote:

Hi everybody!
Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups.

Can I tell phenix.refine not to move only those two residues?

It should be something like the following lines in the eff file?
sites {
      individual = None
      torsion_angles = None
      rigid_body = None

      remove_selection=resid 45

      remove_selection=resid 68

}

Thank you very much
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