[phenixbb] how to refine everything except n residues in phenix.refine?
Pavel Afonine
pafonine at lbl.gov
Fri May 23 08:36:32 PDT 2014
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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