[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


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.


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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